Research ArticleEPIDEMIOLOGY

Reduced evolutionary rate in reemerged Ebola virus transmission chains

See allHide authors and affiliations

Science Advances  29 Apr 2016:
Vol. 2, no. 4, e1600378
DOI: 10.1126/sciadv.1600378
  • Fig. 1 The Needowein flare-up represents the reemergence of an EBOV transmission chain from the Liberian portion of the Western African EVD outbreak.

    (A) Median-joining haplotype network constructed from a full genome alignment of 583 Western African EBOV sequences (see table S3 for accession numbers). The dashed oval indicates the LB2 sublineage (SL2 lineage), which includes the sequences from the Needowein flare-up. Gray shading indicates the lineages that were circulating during February to October 2015 in Sierra Leone and Guinea (GN1, SL3, and SL4). (B) Median-joining haplotype network depicting the LB2 sublineage (see table S3 for accession numbers), including six sequenced genomes from the Barclay Farm cluster during August to September 2014 (purple). See table S1 for a description of the labeled substitutions (a to g).

  • Fig. 2 Several EVD case clusters, including the Needowein flare-up (June to July 2015), are characterized by EBOV with lower-than-expected sequence divergence based on sampling date.

    (A) Root-to-tip distance versus sampling date for the Liberian portion of the SL2 lineage, including sequences from Guinea and Mali linked to reintroductions from Liberia (5). Green, Needowein flare-up; pink, sexual transmission (1); blue, St. Paul Bridge cluster (8); orange, Guinean cluster; dashed lines, 95% prediction interval. (B) Temporal maximum clade credibility tree from BEAST (Bayesian evolutionary analysis by sampling trees). Circles represent sampled EBOV genomes colored as described in (A). For the Needowein flare-up (green) and the March 2015 case of sexual transmission (pink), the dashed lines represent the difference between the actual date of sampling (right) and the estimated sampling date from the BEAST analysis (left). The posterior distributions for the estimated sampling dates are shown below the tree.

  • Table 1 Patient information for sequenced samples ordered by date tested.

    F, female; M, male; ND, not determined.

    Sample IDSexAgeStatusVillageCountySample typeDate testedClusterGenBank accession number
    LIBR20001FNDDeceasedBarclay FarmMargibiBlood10 August 2014Barclay FarmKU220277
    LIBR20002M50DeceasedBarclay FarmMargibiBlood24 August 2014Barclay FarmKU220278
    LIBR20003F20DeceasedBarclay FarmMargibiBlood24 August 2014Barclay FarmKU220279
    LIBR20004M13AliveBarclay FarmMargibiBlood24 August 2014Barclay FarmKU220280
    LIBR20005F4DeceasedBarclay FarmMargibiBlood25 August 2014Barclay FarmKU220281
    LIBR20006F28DeceasedBarclay FarmMargibiBlood25 August 2014Barclay FarmKU220282
    LIBR4748M17DeceasedNeedoweinMargibiOral swab29 June 2015NeedoweinKU220269
    LIBR4783Blood*30 June 2015KU220270
    LIBR4808M23AliveNeedoweinMargibiBlood1 July 2015NeedoweinKU220271
    LIBR4866Blood2 July 2015KU220272
    LIBR5046M40AliveNeedoweinMargibiBlood7 July 2015NeedoweinKU220273
    LIBR5047F13AliveNeedoweinMargibiBlood7 July 2015NeedoweinKU220274
    LIBR5081Blood8 July 2015KU220275
    LIBR5307F22DeceasedPaynesvilleMontserradoBlood12 July 2015NeedoweinKU220276

    *Postmortem heart puncture.

    Supplementary Materials

    • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/2/4/e1600378/DC1

      fig. S1. Median-joining haplotype networks depicting two clusters of EBOV genomes characterized by significantly low levels of genetic divergence (from the root of the Liberian portion of the EVD outbreak) relative to testing date (see Fig. 2A).

      table S1. Substitutions that define the Needowein and Barclay Farm samples (see Fig. 1B).

      table S2. EBOV genomes with lower-than-expected levels of sequence divergence given the testing date (see Fig. 2A).

      table S3. EBOV genomes used in genetic analyses.

      table S4. Sequencing statistics for samples processed for study.

    • Supplementary Materials

      This PDF file includes:

      • fig. S1. Median-joining haplotype networks depicting two clusters of EBOV genomes characterized by significantly low levels of genetic divergence (from the root of the Liberian portion of the EVD outbreak) relative to testing date (see Fig. 2A).
      • table S1. Substitutions that define the Needowein and Barclay Farm samples (see Fig. 1B).
      • table S2. EBOV genomes with lower-than-expected levels of sequence divergence given the testing date (see Fig. 2A).
      • legend for table S3
      • table S4. Sequencing statistics for samples processed for study.

      Download PDF

      Other Supplementary Material for this manuscript includes the following:

      • table S3 (Microsoft Excel format). EBOV genomes used in genetic analyses.

      Files in this Data Supplement:

    Stay Connected to Science Advances

    Navigate This Article