Reduced Evolutionary Rate in Reemerged Ebola Virus Transmission Chains

Overview

Journal Sci Adv

Specialties Biology
Science

Date 2016 Jul 8

PMID 27386513

Citations 45

Authors

David J Blackley

Michael R Wiley

Jason T Ladner

Mosoka Fallah

Terrence Lo

Merle L Gilbert

Christopher Gregory

Jonathan DAmbrozio

Stewart Coulter

Suzanne Mate

Zephaniah Balogun

Jeffrey Kugelman

William Nwachukwu

Karla Prieto

Adolphus Yeiah

Fred Amegashie

Brian Kearney

Meagan Wisniewski

John Saindon

Gary Schroth

Lawrence Fakoli

Joseph W Diclaro 2nd

Jens H Kuhn

Lisa E Hensley

Peter B Jahrling

Ute Stroher

Stuart T Nichol

Moses Massaquoi

Francis Kateh

Peter Clement

Alex Gasasira

Fatorma Bolay

Stephan S Monroe

Andrew Rambaut

Mariano Sanchez-Lockhart

A Scott Laney

Tolbert Nyenswah

Athalia Christie

Gustavo Palacios

Affiliations

Soon will be listed here.

Abstract

On 29 June 2015, Liberia's respite from Ebola virus disease (EVD) was interrupted for the second time by a renewed outbreak ("flare-up") of seven confirmed cases. We demonstrate that, similar to the March 2015 flare-up associated with sexual transmission, this new flare-up was a reemergence of a Liberian transmission chain originating from a persistently infected source rather than a reintroduction from a reservoir or a neighboring country with active transmission. Although distinct, Ebola virus (EBOV) genomes from both flare-ups exhibit significantly low genetic divergence, indicating a reduced rate of EBOV evolution during persistent infection. Using this rate of change as a signature, we identified two additional EVD clusters that possibly arose from persistently infected sources. These findings highlight the risk of EVD flare-ups even after an outbreak is declared over.

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References

Gire S, Goba A, Andersen K, Sealfon R, Park D, Kanneh L . Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. 2014; 345(6202):1369-72. PMC: 4431643. DOI: 10.1126/science.1259657. View

Baize S, Pannetier D, Oestereich L, Rieger T, Koivogui L, Magassouba N . Emergence of Zaire Ebola virus disease in Guinea. N Engl J Med. 2014; 371(15):1418-25. DOI: 10.1056/NEJMoa1404505. View

Bawo L, Fallah M, Kateh F, Nagbe T, Clement P, Gasasira A . Elimination of Ebola Virus Transmission in Liberia - September 3, 2015. MMWR Morb Mortal Wkly Rep. 2015; 64(35):979-80. DOI: 10.15585/mmwr.mm6435a5. View

Drummond A, Ho S, Phillips M, Rambaut A . Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006; 4(5):e88. PMC: 1395354. DOI: 10.1371/journal.pbio.0040088. View

Drummond A, Suchard M, Xie D, Rambaut A . Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012; 29(8):1969-73. PMC: 3408070. DOI: 10.1093/molbev/mss075. View

Varkey J, Shantha J, Crozier I, Kraft C, Lyon G, Mehta A . Persistence of Ebola Virus in Ocular Fluid during Convalescence. N Engl J Med. 2015; 372(25):2423-7. PMC: 4547451. DOI: 10.1056/NEJMoa1500306. View

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

Quick J, Loman N, Duraffour S, Simpson J, Severi E, Cowley L . Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016; 530(7589):228-232. PMC: 4817224. DOI: 10.1038/nature16996. View

Kugelman J, Wiley M, Mate S, Ladner J, Beitzel B, Fakoli L . Monitoring of Ebola Virus Makona Evolution through Establishment of Advanced Genomic Capability in Liberia. Emerg Infect Dis. 2015; 21(7):1135-43. PMC: 4816332. DOI: 10.3201/eid2107.150522. View

10.

Hanada K, Suzuki Y, Gojobori T . A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Mol Biol Evol. 2004; 21(6):1074-80. PMC: 7107514. DOI: 10.1093/molbev/msh109. View

11.

Ladner J, Beitzel B, Chain P, Davenport M, Donaldson E, Frieman M . Standards for sequencing viral genomes in the era of high-throughput sequencing. mBio. 2014; 5(3):e01360-14. PMC: 4068259. DOI: 10.1128/mBio.01360-14. View

12.

Guindon S, Dufayard J, Lefort V, Anisimova M, Hordijk W, Gascuel O . New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010; 59(3):307-21. DOI: 10.1093/sysbio/syq010. View

13.

Carroll M, Matthews D, Hiscox J, Elmore M, Pollakis G, Rambaut A . Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature. 2015; 524(7563):97-101. PMC: 10601607. DOI: 10.1038/nature14594. View

14.

Allela L, Boury O, Pouillot R, Delicat A, Yaba P, Kumulungui B . Ebola virus antibody prevalence in dogs and human risk. Emerg Infect Dis. 2005; 11(3):385-90. PMC: 3298261. DOI: 10.3201/eid1103.040981. View

15.

Norja P, Eis-Hubinger A, Soderlund-Venermo M, Hedman K, Simmonds P . Rapid sequence change and geographical spread of human parvovirus B19: comparison of B19 virus evolution in acute and persistent infections. J Virol. 2008; 82(13):6427-33. PMC: 2447064. DOI: 10.1128/JVI.00471-08. View

16.

Mate S, Kugelman J, Nyenswah T, Ladner J, Wiley M, Cordier-Lassalle T . Molecular Evidence of Sexual Transmission of Ebola Virus. N Engl J Med. 2015; 373(25):2448-54. PMC: 4711355. DOI: 10.1056/NEJMoa1509773. View

17.

Ladner J, Wiley M, Mate S, Dudas G, Prieto K, Lovett S . Evolution and Spread of Ebola Virus in Liberia, 2014-2015. Cell Host Microbe. 2015; 18(6):659-69. PMC: 4711363. DOI: 10.1016/j.chom.2015.11.008. View

18.

Gill M, Lemey P, Faria N, Rambaut A, Shapiro B, Suchard M . Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Mol Biol Evol. 2012; 30(3):713-24. PMC: 3563973. DOI: 10.1093/molbev/mss265. View

19.

Nyenswah T, Fallah M, Sieh S, Kollie K, Badio M, Gray A . Controlling the last known cluster of Ebola virus disease - Liberia, January-February 2015. MMWR Morb Mortal Wkly Rep. 2015; 64(18):500-4. PMC: 4584826. View

20.

Schmieder R, Edwards R . Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011; 27(6):863-4. PMC: 3051327. DOI: 10.1093/bioinformatics/btr026. View