Lassa virus circulating in Liberia: a retrospective genomic characterisation
| Autor: | Michael R. Wiley, Mosoka Fallah, Daniel Reyes, Ute Ströher, Stuart T. Nichol, Karla Prieto, Daniel Negron, Pierre E. Rollin, Tolbert Nyenswah, Nicole Espy, M. Holland, Nicholas Di Paola, Joseph A. Chitty, Shanmuga Sozhamannan, César G. Albariño, Desmond E. Williams, Fatorma K. Bolay, William G. Davis, Catherine B. Pratt, Fahn Taweh, Jason T. Ladner, Ketan Patel, Stephen R. Welch, Gustavo Palacios, Lawrence Fakoli, Andrew G. Letizia, Jon Saindon, John B. Dogba |
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| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Genotype viruses 030106 microbiology Genome Viral Biology medicine.disease_cause Genome Sierra leone 03 medical and health sciences Health surveillance Lassa Fever medicine Humans Public Health Surveillance Lassa virus Lassa fever Clade Phylogeny virus diseases Genomics Biological product Liberia medicine.disease Serum samples Virology 030104 developmental biology Infectious Diseases |
| Zdroj: | The Lancet Infectious Diseases. 19:1371-1378 |
| ISSN: | 1473-3099 |
| DOI: | 10.1016/s1473-3099(19)30486-4 |
| Popis: | Summary Background An alarming rise in reported Lassa fever cases continues in west Africa. Liberia has the largest reported per capita incidence of Lassa fever cases in the region, but genomic information on the circulating strains is scarce. The aim of this study was to substantially increase the available pool of data to help foster the generation of targeted diagnostics and therapeutics. Methods Clinical serum samples collected from 17 positive Lassa fever cases originating from Liberia (16 cases) and Guinea (one case) within the past decade were processed at the Liberian Institute for Biomedical Research using a targeted-enrichment sequencing approach, producing 17 near-complete genomes. An additional 17 Lassa virus sequences (two from Guinea, seven from Liberia, four from Nigeria, and four from Sierra Leone) were generated from viral stocks at the US Centers for Disease Control and Prevention (Atlanta, GA) from samples originating from the Mano River Union (Guinea, Liberia, and Sierra Leone) region and Nigeria. Sequences were compared with existing Lassa virus genomes and published Lassa virus assays. Findings The 23 new Liberian Lassa virus genomes grouped within two clades (IV.A and IV.B) and were genetically divergent from those circulating elsewhere in west Africa. A time-calibrated phylogeographic analysis incorporating the new genomes suggests Liberia was the entry point of Lassa virus into the Mano River Union region and estimates the introduction to have occurred between 300–350 years ago. A high level of diversity exists between the Liberian Lassa virus genomes. Nucleotide percent difference between Liberian Lassa virus genomes ranged up to 27% in the L segment and 18% in the S segment. The commonly used Lassa Josiah-MGB assay was up to 25% divergent across the target sites when aligned to the Liberian Lassa virus genomes. Interpretation The large amount of novel genomic diversity of Lassa virus observed in the Liberian cases emphasises the need to match deployed diagnostic capabilities with locally circulating strains and underscores the importance of evaluating cross-lineage protection in the development of vaccines and therapeutics. Funding Defense Biological Product Assurance Office of the US Department of Defense and the Armed Forces Health Surveillance Branch and its Global Emerging Infections Surveillance and Response Section. |
| Databáze: | OpenAIRE |
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