Decentralised sequencing for infectious disease surveillance

Project summary

Climate change is estimated to cause 250,000 additional deaths per year between 2030 and 2050, a significant proportion of which will be due to diarrhoeal diseases and infections caused by pathogens transmitted by climate-sensitive vectors affected by increasing temperatures and extreme weather events.
Tanzania’s diverse climate and topography presents a favourable context for studies into the differential risks of climate-sensitive pathogens, but currently lacks a robust system that can rapidly detect, identify, track and share information on (re)-emerging pathogens. This both limits its ability to respond to outbreaks, and impedes the analysis of long-term changes and trends needed to establish preventive policy measures.
Advances in sequencing have enabled rapid identification of complete genomic information of pathogens. ONT sequencers have demonstrated to be particularly useful in resource-limited settings because of their portability, low up-front costs and feasibility for real-time outbreak tracking of recent epidemics (e.g. Ebola, Zika and COVID-19). It has as well been used for rapid identification of bacterial infections and AMR of clinical relevance. This project proposes to create the capacity for ONT-based sequencing, analyse and real-time sharing of pathogen information at selected research centres across Tanzania. The implementation will focus on climate-sensitive and epidemic-prone pathogens that cause acute febrile illnesses and childhood diarrhoea, while creating the capacity for all-round genomics and bioinformatics work at these research centres. Finally, the project will create integrated epidemiological, meteorological and genomic databases that can be used for retrospective retrieval and analysis.
The project builds on a previous DANIDA-research funded collaboration whereby a sustainable genomics & bioinformatics unit at KCRI was established. This will form the backbone for the decentralised ’sequencing at the source’ capacity realised in this project.

Outputs

First year report:
16th April 2021 in Dodoma: Project kickoff meeting attended by all project partners and the NIMR director general.
14th Sept 2021 in Dodoma: Consultative and planning meeting attended by medical officers in charge from 5 participating hospitals and director of curative and preventive services ministry of health.
19th to 23rd April 2021 in Moshi: A one-week hands on training on sequencing and analysis was conducted at KCRI. Twelve lab technicians (2 @ hospital) from all participating hospitals were trained.
17 June 2022 in Dodoma. Live sequencing performed and demonstrated by all participating regional laboratories to invited stakeholders.
Two ethical approvals from Zanzibar (ZAHRI) and Tanzania mainland (NIMR) to allow project implementation were obtained since February 2022. Additionally the project has received permission from Regional Administration and Local Government (TAMISEMI) to allow regional hospitals in Tanzania mainland to participate.
Two PhDs are registered - one will characterise climate senistive viral pathogens in blood/stool and the other will characterise bacteria in blood/stool. Two MSc fellows are are pursuing molecular biology and one MSc fellow is doing biostatistics. All fellows are registered in local universities. The fellows are an integral part in the project implementation. All sites have been visited, trained and are implementing the project at different levels of expertise.