Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases

Abstract

To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Phylogenetic analysis of complete EBOV genomes can provide important information on the source of any new infection. A local deep sequencing facility was established at the Mateneh Ebola Treatment Centre in central Sierra Leone. The facility included all wetlab and computational resources to rapidly process EBOV diagnostic samples into full genome sequences. We produced 554 EBOV genomes from EVD cases across Sierra Leone. These genomes provided a detailed description of EBOV evolution and facilitated phylogenetic tracking of new EVD cases. Importantly, we show that linked genomic and epidemiological data can not only support contact tracing but also identify unconventional transmission chains involving body fluids, including semen. Rapid EBOV genome sequencing, when linked to epidemiological information and a comprehensive database of virus sequences across the outbreak, provided a powerful tool for public health epidemic control efforts.

Keywords: Ebola virus; evolution; outbreak sequencing; transmission.

Figure 1.

Lineages circulating in sampled regions. Districts of Sierra Leone (blue), Guinea (green), and Liberia (orange) are indicated. Pie charts are drawn over districts from which samples of this study were collected, with size relative to the number of samples, and segment area indicating the proportion of lineages (as defined in Figure 2) observed at that location. The number of genomes from each location was the following: Bombali: 63, Kambia: 67, Koinadugu: 5, Port Loko: 98, Tonkolili: 4, Western Area: 182, Unknown location: 135.

Figure 2.

Maximum-likelihood tree showing the phylogenetic context of the viruses sequenced in this study. The 554 genomes generated here are shown as red circles, while the nine comprising lineages are highlighted with colored boxes and labeled A–H for those derived from the SL3 lineage, or GUI-1 for viruses derived from the divergent Guinean lineage. The tree was rooted on Gueckedou-C05 (GenBank accession no. KJ660348), with the scale bar indicating genetic distance in units of substitutions/site. Specific genomes in the three transmission vignettes (see Fig. 3), MK8878, 19560_EMLK, and PL9192c are highlighted.

Figure 3.

(a) Mamusa Cluster timeline. Key events in the Mamusa cluster examined in (b) are summarized. (b) Maximum-likelihood tree of the Mamusa cluster showing the phylogenetic relationship between each case's virus genome. The genome from the case A breast milk sample (PL9192, labeled in red, GenBank accession no. KU296401) is highlighted in red. Additional cases in the cluster include the earlier case B (most probable index case of the cluster, GenBank accession no. KU296340); case C (the 6 day-old newborn daughter of B, GenBank accession no. KU296618), and D (sister of B, includes two viruses sampled 3 d apart, GenBank accession nos. KU296404 and KU296342). Contacts of A include cases E (13 month-old daughter of A, GenBank accession no. KU296522) and F (sister of A, GenBank accession no. KU296371). Bootstrap support values greater than 50% are given below the respective node. The bar colors on the right indicate the place of sampling of each virus (legend is shown on the left). All mutations within the case cluster are given above the relevant branch as the position in the original alignment followed by the nucleotide change. The scale bar indicates the genetic distance in units of substitutions/site.

Figure 4.

Maximum-likelihood tree showing that the Tonkolili case derived from the Magazine Wharf lineage. The Tonkolili index case G (MK8878, labeled in red, GenBank accession no. KU296684) was derived from a clade of viruses circulating predominantly in Magazine Wharf, and clusters with the two secondary Tonkolili secondary cases H (G’s brother, GenBank accession no. KU296502) and J (G’s aunt, GenBank accession no. KU296313). See legend of Fig. 3(a) for additional figure details.

Figure 5.

(a) Maximum-likelihood tree showing the Kambia cluster with possible sexual transmission and full genome from a semen sample. The virus from case L’s initial acute sample (19560R_EMLK, GenBank accession no. KU296580) is the most probable index case of the Kambian cluster. After a 21-d period of quarantine, case L was discharged on 18 July 2015. A sample from case L’s semen (19560_EMLK, labeled in red, GenBank accession no. KU296821) was collected on 7 September 2015. The virus genome isolated from the deceased case K (020380_EMLK, GenBank accession no. KU296775) is genetically identical to case L, which also clusters closely with case M (K’s 23-year-old daughter, 20525_EMLK, GenBank accession no. KU296487). For each cluster case, minority variants for three key positions can be found in (b). Symptom onset of case M (3 September 2015) was 15 d later than onset of case K (26 August 2015). Case K is genetically identical to three known contacts of K: case N (020484_EMLK, older daughter of K, GenBank accession no. KU296462), case O (20547_EMLK, sister of K, GenBank accession no. KU296455), case P (20524_EMLK, grandchild of K, GenBank accession no. KU296424). Case Q (20573_EMLK, GenBank accession no. KU296654), also from the same village, is the most recent sampled case from this cluster. The lineage is related to earlier viruses from lineage F (19521_EMLK, 15543_EMLK, KT7095, and 15421_EMLK, see Fig. 2). See legend of Fig. 3(b) for additional figure details. (b) Minor variants in the Kambia lineage. In genomes from the Kambia cluster (a) three genome positions (3993, 8494, and 13518) showed changes across the entire lineage leading from 19521 through to all genomes in the family cluster. The presence of each of the two variant nucleotides was counted in the raw read set for each sample to gain additional information about possible transmission patterns. Positions with minor variants at >1% frequency are marked with a red asterisk. Positions 3994, 8496, and 13520 showed mixed nucleotides in samples from cases K and M, similar to the case L semen sample (but not in the case L initial sample). Later cases in the lineage (N–Q) showed predominately one of the variants at each of the three positions, although position 13520 showed some persistence of the minor variant C. These data further support the phylogenetic conclusions based on the consensus genome sequence with the L semen sample containing minor variants at the three positions that increase in frequency in samples from cases K and M and become the dominant nucleotide in cases N–Q.