Surveillance and agnostic capture sequencing of samples from individuals with rash-associated illness in Mali indicates regional transmission of measles virus from West and Central Africa
Measles is vaccine-preventable extremely contagious disease caused by the measles virus. High vaccination coverage is needed to prevent outbreaks of disease. Although molecular surveillance of measles is critical to characterize outbreaks and track viral evolution, few whole-genome sequences of measles virus from West Africa are available despite continual outbreaks in the region. Using VirCapSeq-VERT, an enhanced and comprehensive metagenomic sequencing technique that allows for simultaneous identification of all vertebrate viruses, 23 wild-type near-complete genomes of measles virus from across Mali were obtained from samples collected between January 2012 to October 2022. Other febrile rash illnesses were also identified by VirCapSeq-VERT, demonstrating the advantage of using broad detection agnostic methods when the clinical diagnosis is unclear. Whereas one measles virus sequence was consistent with measles vaccine-associated rash illness (VARI), the remaining 38 were classified within the B3.1 genotype. Broad surveillance throughout Mali reveals regional measles virus transmission across West and Central Africa into Mali, while local clinical testing in Bamako shows stable sequence conservation within genotype B3.1 evolving from Nigerian sequences. The genomic information generated in this study is critical in addressing the lack of whole genome sequences available in West Africa and these findings show the importance of phylogenetically tracking measles outbreaks given recent increases in measles cases globally.
Authors
- Kathryn Saliba-Shaw
- Ray Y. Chen (ORCID: https://orcid.org/0000-0001-6344-1442)
- Thomas Briese (ORCID: https://orcid.org/0000-0002-4819-8963)
- John P. Collins (ORCID: https://orcid.org/0000-0002-5957-6923)
- A. Koné (ORCID: https://orcid.org/0000-0002-6736-3653)
- Ibréhima Guindo (ORCID: https://orcid.org/0000-0003-3130-4763)
- Ibrahim Sanogo (ORCID: https://orcid.org/0000-0001-9800-9369)
- Bassirou Diarra (ORCID: https://orcid.org/0000-0002-1795-9379)
- Korotoumou Koné
- Aaron Neal (ORCID: https://orcid.org/0000-0001-7674-0038)
- Dramane Diallo (ORCID: https://orcid.org/0000-0001-9761-3652)
- Djénéba Dabitao (ORCID: https://orcid.org/0000-0001-5150-6990)
- Namory Keita
- Jamila Aboulhab
- J. Kenneth Wickiser (ORCID: https://orcid.org/0000-0002-5034-2100)
- Issa Cisse
- Fousseyni Kané
- Mountaga Diallo (ORCID: https://orcid.org/0009-0001-3543-7451)
- Cheick Oumar Tangara
- Toua Antoine Coulibaly
- I Konaté (ORCID: https://orcid.org/0000-0003-2086-0019)
- Xiang‐Jun Lu (ORCID: https://orcid.org/0000-0002-8901-7444)
- Walter Ian Lipkin (ORCID: https://orcid.org/0000-0002-8768-9386)
- Mahamadou Diakité (ORCID: https://orcid.org/0000-0002-4268-8857)
- Sounkalo Dao
- Daouda Keita
- Seydou Doumbia (ORCID: https://orcid.org/0000-0003-1637-5600)
- Karine Fouth-Tchos
Institutions
- Institut National de Recherche en Santé Publique (ML)
- Université des Sciences, des Techniques et des Technologies de Bamako (ML)
- National Institute of Allergy and Infectious Diseases (US)
- Columbia University (US)
Publication Details
- Journal
- Infection Genetics and Evolution
- Published
- 2024-11-20
- DOI
- https://doi.org/10.1016/j.meegid.2024.105691
- Primary Topic
- Virology and Viral Diseases
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- U.S. Department of Health and Human Services
- Leidos
- Skoll Foundation
- National Institutes of Health
- National Cancer Institute
- National Institute of Allergy and Infectious Diseases