Characterising the virus composition of outbreaks of non-malaria acute febrile illness (NM-AFI)

Reference Number: 
Type of project: 


The Tanzanian government has recently established the Preparedness and Response Unit (PRU) under the Prime Minister’s Office []. This unit conducts surveillance of emerging and re-emerging diseases which are likely to cause emergencies, to assist in appropriate responses, identify origins and spread and identify risk factors for predisposing to possible outbreaks. However, the unit lacks the necessary diagnostic capacity to assess the composition and source of outbreaks. There are periodic outbreaks of non-malarial acute febrile illnesses for which the aetiology is not established. This is in part due to absence of adequate surveillance and response diagnostic capacity. For example, in a recent large outbreak of acute febrile illness in rural Tanzania (Korogwe 2017), only a small percentage was due to malaria (10-12%, unpublished), and the definitive cause has yet to be identified. It is suspected that arboviruses, such as dengue and chikungunya, are of importance as has been shown when intensive surveillance has been undertaken (Chipwaza et al. 2014; Crump et al. 2013). KCRI has stored 600 blood samples together with associated clinical, treatment, demographic, geo-spatial and outcome data. WGS offers benefits in resolving transmission details at the local level and enables possible identification of virus origin and route into the community: shown in recent times for zika, ebola and rabies viruses (Faria et al. 2016; Gire et al. 2014).

The project aims to:

  1. Develop genomic and bioinformatics capacity to diagnose outbreaks of non-malarial AFI
  2. Identify the viral composition from archived samples from the outbreak in Korogwe District, NE Tanzania
  3. Establish a database of arbovirus genomes to use as a basis of future phylogeographic studies and predictions

Methods/Study design:

This project will use metagenomic approach to identify viruses in blood samples using sets of samples pooled by geographic location. Alternatively, primers sets targeted to families of viruses (eg Flaviviridae) can be used to develop amplicon based methods. The work will initially be developed using the Illumina MiSeq platform as there is already support from within the Partners to establish. Six hundred blood samples were collected from residents of different wards of Korogwe district between April and July 2017.

The outputs will be:

  1. Establish the sequencing and bioinformatics pipeline for assessing the composition of viruses from AFI outbreaks.
  2. Provision of findings to the PRU and a database of genomes placed on Open Access
  3. Produce a local distributional map of this outbreak as a start to building a national spatio-temporal database of viruses across the country
  4. Intention to establish a permanent link between DPRU and KCRI for provision of outbreak characterisation

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)

Viral causes of acute febrile illness are under-diagnosed in Tanzania, particularly dengue and chikungunya. Data will be deposited in a database that will be made freely accessible by the Ministries of Health and Livestock through the PRU of the Prime Minister’s Office. This will be readily possible since Drs Ireen Kiwelu and Jaffu Chilongola from KCRI are members of the Technical Work Groups (TWG) of the PRU. According to the PRU’s strategic plan, access of data from the proposed project will facilitate development of plans and policy on surveillance and control of priority viral infections including arbovirus outbreaks.


Chipwaza,B., Mugasa,J.P., Selemani,M., Amuri,M., Mosha,F., Ngatunga,S.D. and Gwakisa,P.S. (2014). Dengue and Chikungunya fever among viral diseases in outpatient febrile children in Kilosa district hospital, Tanzania. PLoS neglected tropical diseases 8(11):e3335.

Crump,J.A., Morrissey,A.B., Nicholson,W.L., Massung,R.F., Stoddard,R.A., Galloway,R.L., Ooi,E.E., Maro,V.P., Saganda,W. and Kinabo,G.D. (2013). Etiology of severe non-malaria febrile illness in Northern Tanzania: a prospective cohort study. PLoS neglected tropical diseases 7(7):e2324.

Faria,N.R., da Silva Azevedo,R.d.S., Kraemer,M.U., Souza,R., Cunha,M.S., Hill,S.C., Th+¬z+¬,J., Bonsall,M.B., Bowden,T.A. and Rissanen,I. (2016). Zika virus in the Americas: early epidemiological and genetic findings. Science :aaf5036.

Gire,S.K., Goba,A., Andersen,K.G., Sealfon,R.S., Park,D.J., Kanneh,L., Jalloh,S., Momoh,M., Fullah,M. and Dudas,G. (2014). Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science :1259657.