Virus genomes reveal factors that spread and sustained the Ebola epidemic

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Abstract

Frequent dispersal and short-lived local transmission clusters fuelled the 2013–2016 Ebola virus epidemic in Guinea, Liberia and Sierra Leone.

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Most cited references 28

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Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci.

Mandev S Gill, Philippe Lemey, Nuno Faria … (2013)

Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a Gaussian Markov random field (GMRF) model for a single gene locus. Here, we present a generalization of the GMRF model that allows for the analysis of multilocus sequence data. Using simulated data, we demonstrate the improved performance of our method to recover true population trajectories and the time to the most recent common ancestor (TMRCA). We analyze a multilocus alignment of HIV-1 CRF02_AG gene sequences sampled from Cameroon. Our results are consistent with HIV prevalence data and uncover some aspects of the population history that go undetected in Bayesian parametric estimation. Finally, we recover an older and more reconcilable TMRCA for a classic ancient DNA data set.

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An unwinding activity that covalently modifies its double-stranded RNA substrate.

Eric Bass, H Weintraub (1988)

An activity that unwinds double-stranded RNA has been reported to exist in several organisms. We have analyzed the RNA intermediates and final products of the unwinding reaction. Although the RNA becomes sensitive to single strand-specific ribonucleases during the reaction, the duplex is never completely unwound. Furthermore, the base pairing properties of the RNA are permanently altered; the reacted RNA cannot rehybridize to form the original duplex. We demonstrate that during the reaction many, but not all, of the adenosine residues are converted to inosine residues, and we propose that the covalent modification is responsible for the irreversible change in base pairing properties. Possible biological roles for the unwinding/modifying activity, as well as its relevance to antisense RNA experiments, are discussed.

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The dynamics of measles in sub-Saharan Africa.

Rebecca F. Grais, Ali Djibo, Lara J. Wolfson … (2008)

Although vaccination has almost eliminated measles in parts of the world, the disease remains a major killer in some high birth rate countries of the Sahel. On the basis of measles dynamics for industrialized countries, high birth rate regions should experience regular annual epidemics. Here, however, we show that measles epidemics in Niger are highly episodic, particularly in the capital Niamey. Models demonstrate that this variability arises from powerful seasonality in transmission-generating high amplitude epidemics-within the chaotic domain of deterministic dynamics. In practice, this leads to frequent stochastic fadeouts, interspersed with irregular, large epidemics. A metapopulation model illustrates how increased vaccine coverage, but still below the local elimination threshold, could lead to increasingly variable major outbreaks in highly seasonally forced contexts. Such erratic dynamics emphasize the importance both of control strategies that address build-up of susceptible individuals and efforts to mitigate the impact of large outbreaks when they occur.

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Journal

Title: Nature

Abbreviated Title: Nature

Publisher: Springer Nature

ISSN (Print): 0028-0836

ISSN (Electronic): 1476-4687

Publication date Created: April 12 2017

Publication date (Print): April 12 2017

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DOI: 10.1038/nature22040

PMC ID: 5712493

PubMed ID: 28405027

SO-VID: 68325590-d21e-4bb5-a216-a8771390a6f9

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Virus genomes reveal factors that spread and sustained the Ebola epidemic

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Most cited references 28

Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci.

An unwinding activity that covalently modifies its double-stranded RNA substrate.

The dynamics of measles in sub-Saharan Africa.

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