Establishing rabies genomic sequencing capacity and reference repository for East Africa

Background:

Rabies is an important public health problem in East Africa. About 45% of the 60,000 annual fatal human cases globally, occur in Africa; around 2,000 per annum in Kenya, and 1,500 in Tanzania. It is recognized amongst zoonoses of highest priority(1, 2). National rabies elimination programmes are prepared and active(2, 3). Case surveillance forms an important part of control programmes. Determination of whole genomes can identify the source and transmission pathway of the virus, and in the case of rabies WGS is more discriminative than partial gene sequencing(4). In a Tanzanian study it has been Role of /links with National / Local Public-Health Organisation
(including access to data, sources of samples, role in defining question and potential impact on policy)shown that rabies virus distribution in dogs tends to be localized with little cross-boundary transmission: information important to control prospect (5). As yet, there are very few genome sequences available by which to compare incident cases and explore geographic partitioning across East Africa. There is little capacity for whole genome sequencing in East Africa. Whole genome sequencing NGS methods are developed for the Illumina MiSeq platform(5, 6). In addition, of recent a rapid and low-cost method has been developed based on the Oxford Nanopore MinION platform. We are in communication with the Glasgow research group who developed the method, and staff from Partner Institutes are attending a Nanopore workshop in Ghana in December 2018. Future research studies will focus on investigating the transmission patterns of the virus based on the growing sequence database across the Region. The project aims to: (i) Transfer the rapid and cost-effective Nanopore MinION rabies WGS technique to KCRI, Tanzania (ii) Sequence archived rabies virus positive samples from across the Region. Methods: Initial training in use of Nanopore in December 2018. Transfer technology to Partner sites (UVRI/ KCRI/ KWTRP). Utilize existing samples from rabid animals stored at National Veterinary Labs, as well as human samples from KCMC and UVRI. The outputs will be: (i) Established sequencing capacity that can be employed by public health authorities for incident cases (ii) An expanded geocoded sequence repository against which to compare human and animal cases. (iii) Collaborative links set up with research scientists involved in rabies phylogeography, eg University of Glasgow.

The project aims to:

1. Transfer the rapid and cost-effective Nanopore MinION rabies WGS technique to KCRI, Tanzania
2. Sequence archived rabies virus positive samples from across the Region.

Methods:

Initial training in use of Nanopore in December 2018. Transfer technology to Partner sites (UVRI/ KCRI/ KWTRP). Utilize existing samples from rabid animals stored at National Veterinary Labs, as well as human samples from KCMC and UVRI.

The outputs will be:

1. Established sequencing capacity that can be employed by public health authorities for incident cases
2. An expanded geocoded sequence repository against which to compare human and animal cases.
3. Collaborative links set up with research scientists involved in rabies phylogeography, eg University of Glasgow.

Role of /links with National / Local Public-Health Organisation
(including access to data, sources of samples, role in defining question and potential impact on policy)

• Priority advice and policy issues – discussions with Dr John Stephen Kunda, National Technical Advisor, One Health, Preparedness and Response Unit (PRU) at Prime Minister’s Office Rabies is rated in top 5 priority zoonotic diseases.
• Drs Ireen Kiwelu and Jaffu Chilongola from KCRI are on the Advisory Board of the PRU
• Availability of rabies virus positive samples from National Veterinary Laboratories, and KCRI and UVRI
• Locally, in Tanzania, Moshi District environmental health officer has announced plans to start culling bats, but is eager to base policy on evidence and assess rabies prevalence and transmission.

References:

1. CDC Tanzania. One Health Zoonotic Disease Prioritization for Multisectoral Engagement in Tanzania March 23-24 2017, Accessed 18/10/2018 [Available from: https://www.cdc.gov/onehealth/pdfs/tanzania-report-508.pdf.
2. ZDU Zoonotic Disease Unit Kenya. National rabies elimination strategy Accessed 18/10/2018 [Available from: http://zdukenya.org/programme-1/.
3. WHO. Rabies Control in Tanzania Accessed 18/10/2018 [Available from: http://www.who.int/rabies/control/Tanzania_Project_Summary_310317.pdf
4. Nadin-Davis SA, Colville A, Trewby H, Biek R, Real L. Application of high-throughput sequencing to whole rabies viral genome characterisation and its use for phylogenetic re-evaluation of a raccoon strain incursion into the province of Ontario. Virus research. 2017;232:123-33.
5. Brunker K, Marston DA, Horton DL, Cleaveland S, Fooks AR, Kazwala R, et al. Elucidating the phylodynamics of endemic rabies virus in eastern Africa using whole-genome sequencing. Virus evolution. 2015;1(1):vev011.
6. Hanke D, Freuling CM, Fischer S, Hueffer K, Hundertmark K, Nadin-Davis S, et al. Spatio-temporal Analysis of the Genetic Diversity of Arctic Rabies Viruses and Their Reservoir Hosts in Greenland. PLoS neglected tropical