Monitoring of Ebola Virus Makona Evolution through Establishment of Advanced Genomic Capability in Liberia - Volume 21, Number 7—July 2015 - Emerging Infectious Disease journal - CDC

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Monitoring of Ebola Virus Makona Evolution through Establishment of Advanced Genomic Capability in Liberia - Volume 21, Number 7—July 2015 - Emerging Infectious Disease journal - CDC

Volume 21, Number 7—July 2015

Research

Monitoring of Ebola Virus Makona Evolution through Establishment of Advanced Genomic Capability in Liberia

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• Materials and Methods
• Results
• Discussion
• Suggested Citation

Figures

• Figure 1
• Figure 2

Tables

• Table 1
• Table 2
• Table 3

Technical Appendicies

• Technical Appendix 1
• Technical Appendix 2
• Technical Appendix 3

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Jeffrey R. Kugelman1, Michael R. Wiley1, Suzanne Mate1, Jason T. Ladner1, Brett Beitzel, Lawrence Fakoli, Fahn Taweh, Karla Prieto, Joseph W. Diclaro, Timothy Minogue, Randal J. Schoepp, Kurt E. Schaecher, James Pettitt, Stacey Bateman, Joseph Fair, Jens H. Kuhn, Lisa Hensley, Daniel J. Park, Pardis C. Sabeti, Mariano Sanchez-Lockhart, Fatorma K. Bolay, Gustavo Palacios , and on behalf of US Army Medical Research Institute of Infectious DiseasesNational Institutes of HealthIntegrated Research Facility–Frederick Ebola Response Team 2014–2015

Author affiliations: US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA (J.R. Kugelman, M.R. Wiley, S. Mate, J.T. Ladner, B. Beitzel, K. Prieto, T. Minogue, R.J. Schoepp, K.E. Schaecher, S. Bateman, M. Sanchez-Lockhart, G. Palacios); Liberian Institute for Biomedical Research, Charlesville, Liberia (L. Fakoli, F. Taweh, F.K. Bolay); Naval Medical Research Unit 3, Cairo, Egypt (J.W. Diclaro);Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick (J. Pettitt, J.H. Kuhn, L. Hensley); Foundation Merieux, Washington, DC, USA (J. Fair); Broad Institute, Cambridge, Massachusetts, USA (D.J. Park, P.C. Sabeti); Center for Systems Biology, Harvard University, Cambridge (P.C. Sabeti)

Suggested citation for this article

Abstract

To support Liberia’s response to the ongoing Ebola virus (EBOV) disease epidemic in Western Africa, we established in-country advanced genomic capabilities to monitor EBOV evolution. Twenty-five EBOV genomes were sequenced at the Liberian Institute for Biomedical Research, which provided an in-depth view of EBOV diversity in Liberia during September 2014–February 2015. These sequences were consistent with a single virus introduction to Liberia; however, shared ancestry with isolates from Mali indicated at least 1 additional instance of movement into or out of Liberia. The pace of change is generally consistent with previous estimates of mutation rate. We observed 23 nonsynonymous mutations and 1 nonsense mutation. Six of these changes are within known binding sites for sequence-based EBOV medical countermeasures; however, the diagnostic and therapeutic impact of EBOV evolution within Liberia appears to be low.

The outbreak of Ebola virus disease (EVD) in Western Africa that started in November 2013 (1) is the largest recorded filovirus disease outbreak. As the outbreak continues, public health and emerging infectious disease officials have declared a continuing need for real-time monitoring of Ebola virus (EBOV) evolution (2,3). As of March 11, 2015, a total of 41% of reported cases had been fatal (4). By the end of March 2015, the intensity of the outbreak, which throughout its course affected 6 Western Africa countries, appeared to be receding, with near 0 activity in Liberia and no cases in Mali, Nigeria, and Senegal. However, EBOV continues to spread in Guinea and Sierra Leone. The epidemic is still causing more infections per week than have been recorded in previous EVD outbreaks (5). Therefore, public health officials continue to use media to maintain public awareness, to advocate for diligent handwashing and use of other protective measures, and to avoid complacency that could lead to reemergence (5). Vigilance is of paramount importance because currently used assays for EVD diagnosis, and many medical countermeasures in development, were designed using EBOV reference genome variants from previous outbreaks (6–9). Therefore, monitoring EBOV genomic drift is crucial because genetic changes can affect the efficacy of sequence-based therapeutics and diagnostics.

The size and spread of the current EVD outbreak reinforces the need to build public health infrastructure, including state-of-the-art diagnostic and surveillance capabilities, to implement and maintain effective EVD monitoring, treatment, and prevention platforms. The Liberian Institute for Biomedical Research (LIBR), established in 1975, is located in Charlesville, 50 km southeast of Liberia’s capital, Monrovia. As of April 2, 2015, it is one of the few local facilities within Liberia processing clinical samples from persons suspected to have EVD. A consortium comprising US government and nongovernment agencies has been working with the Liberian government to equip LIBR with advanced genomic sequencing capabilities. These capabilities are dedicated primarily to EVD surveillance activities, including genome sequencing of EBOV-positive samples. The new LIBR Genome Center has a Miseq sequencer (Illumina, San Diego, CA, USA) and ancillary supporting capabilities, including electrophoresis for qualification, fluorometry for quantitation, PCR for amplification, and fully functional computational analysis capabilities to perform pathogen discovery and microbial genome characterization. The US Army Medical Research Institute of Infectious Diseases (USAMRIID) Center for Genome Sciences supports LIBR operation and development. Sample preparation procedures under biosafety containment are provided within the same building complex by the Liberian National Reference Laboratories, operated by USAMRIID and the National Institutes of Health Integrated Research Facility Ebola Response Team (Fort Detrick, Frederick, MD, USA). Throughput at the LIBR Genome Center is 10–20 samples (≈10 billion bases of sequence data) per week, with a target turnaround time of 7 days from sample receipt for high-priority samples. To ensure long-term sustainment of surveillance-based sequencing capabilities, local biomedical scientists have been trained and can proficiently perform all daily activities.

Here we demonstrate the utility and capabilities of the LIBR Genome Center. With the immediate goal of continuing the natural history characterization of the EBOV Makona variant (EBOV/Mak [10]) currently circulating in Western Africa and to support ongoing clinical trials to evaluate candidate medical countermeasures, we describe 25 EBOV genome sequences from the first 5 sequencing runs conducted at the LIBR Genome Center. We chose these samples for full-genome characterization from ≈1,700 available samples on the basis of high viral load (cycle threshold [Ct]) value <24) and date of collection to ensure up-to-date temporal coverage.

Dr. Kugelman is a biodefense research scientist, computational biologist, and head of Bioinformatics at the Center for Genome Sciences at USAMRIID. His research interests include the genomic study of filovirus and orthopoxvirus infections.

Acknowledgments

We thank Matthew A. Voorhees, Brian J. Kearney, Gary W. Carter, Jason Kindrachuk, Anthony R. Jones, Alex Hail, Alissa L. Byrne, Melissa A. Dugan, Mark M. Bailey, Krisztina Janosko, Joanna Fishback, Joshua Johnson, Richard Bennett, Susana Padilla, Michelle A. Jefferson, Jonathan Marchand, and Michael R. Holbrook for providing the infrastructure, isolation of viral genomic material, and Ebola diagnostic screening on which this study is built. We thank Aaron T. Momolu, Josiah S. George, Charlesetta Kanneh, Vera Yatta Walker, and Augustine Fallah for their help, support, and enthusiasm. We thank Neal Woollen, Dave Norwood, and Peter Jahrling for their full support on this endeavor. We also thank Deborah R. Malac for her support of the USAMRIID and NIH/IRF Ebola Response Team; Tabitha Austill for arranging the shipment of equipment and supplies to LIBR; and Sean Lovett and Brad Pfeffer for the expedited deposition of sequence data in public repositories. We also thank Laura Bollinger for providing technical writing services.

This work was supported by Defense Threat Reduction Agency, the Global Biosurveillance Technology Initiative, the US Agency for International Development, and Illumina.

J.H.K. performed this work as an employee of Tunnell Government Services, Inc., a subcontractor to Battelle Memorial Institute under its prime contract with the National Institute of Allergy and Infectious Diseases, under contract no. HHSN272200700016I.

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Figures

• Figure 1. A) Median-joining haplotype network constructed from a full-genome alignment of 122 clinical Ebola virus Makona (EBOV/Mak) isolates (list of isolates in Technical Appendix 3). Each colored vertex...
• Figure 2. Mutation analysis of candidate therapeutic drug and diagnostic binding sites used in outbreak of Ebola virus (EBOV) disease, Western Africa. A single-nucleotide polymorphism (SNP) table is combined with a...

Tables

• Table 1. Characteristics of Ebola virus samples from selected patients, Liberia, September 2014–February 2015
• Table 2. Next-generation sequencing of 25 Ebola virus isolates derived from selected patients sampled, Liberia, September 2014–February 2015
• Table 3. Mutation analysis of candidate therapeutic drug and diagnostic binding sites for EBOV

Technical Appendices

• Technical Appendix 1. Map of Liberia counties showing the 25 Ebola virus (EBOV) isolates described in this study; mutation analysis of diagnostic binding sites; and diagnostic probe information.  362 KB
• Technical Appendix 2. Consensus-level variants in 25 Liberian Ebola virus Makona genomes relative to reference genome Ebola virus/H.sapiens-wt/GIN/2014/Makona-C15.  17 KB
• Technical Appendix 3. Ebola virus Makona isolates used in genetic analyses.  15 KB

Suggested citation for this article: Kugelman JR, Wiley MR, Mate S, Ladner JT, Beitzel B, Fakoli L, et al. Monitoring of Ebola virus Makona evolution through establishment of advanced genomic capability in Liberia. Emerg Infect Dis. 2015 Jul [date cited]. http://dx.doi.org/10.3201/eid2107.150522

DOI: 10.3201/eid2107.150522

1These authors contributed equally to this article.