Summary

The proposed research aims to increase capacity for molecular-based diagnostics performed on acute clinical samples from patients admitted to hospital with acute undifferentiated febrile illness (AUFI) in Sri Lanka. This will significantly improve management of individual patients, allow optimization of clinical algorithms, admission protocols and stewardship of antimicrobials. We will assess feasibility and utility of molecular diagnostics for AUFI in our local setting. Having established clinical and microbiological workflows through the proposed study, we aim to recruit patients from other Provinces in Sri Lanka. Based upon knowledge of local strain genotypes acquired from sequencing, primer +/- probe design of PCR-based diagnostics for leptospirosis, rickettsiosis and hantavirus can also be optimised. This study will enhance understanding of epidemiology and seasonality of AUFI and downstream benefits include development of prevention strategies, ranging from flu vaccination to optimized control of specific vector/reservoirs. Confirmation of diagnoses with laboratory testing should be in tandem with laboratory notification to a central surveillance unit like the Epidemiology Unit to describe infectious aetiologies circulating in the region during a specific time period and to detect and guide outbreak response.
This study will also provide a meticulously curated biobank for future novel pathogen discovery studies involving metagenomics approaches

Objectives

1. To recruit a cohort of adult and paediatric patients hospitalized secondary to AUFI (exclusive of predominantly respiratory symptoms) in varying geographical regions, temperature, rainfall and topography, representative of different ecological niches, and to establish a biobank of optimally taken and processed samples for PCR diagnostic tests
2. To establish in-house pan-genus PCR diagnostics for dengue, leptospira, rickettsia, and
hantavirus* utilizing published genome targets
3. To carry out sequential testing for AUFI pathogens (dengue, leptospira, rickettsia, hantavirus and influenza) based upon a diagnostic algorithm utilizing PCR tests, supplemented by serologybased tests [enzyme linked immunoassay (ELISA), immunofluorescence assay (IFA),
immunochromatographic test (ICT) or microscopic agglutination test (MAT)] for enhanced
diagnostic sensitivity.
4. To sequence amplicons from conventional PCR and perform phylogenetic analyses of local
pathogenic strains for leptospira, rickettsia and hantavirus
5. To collect supporting epidemiological data to identify associated factors for identified/unknown AUFI pathogen

Major Equipment Facilitated by Grant