New research reveals hidden pathogens behind fever cases in Nigeria

RTI-led surveillance uncovers first recorded human Rickettsial infections in Nigeria and widespread coinfections among febrile patients

RESEARCH TRIANGLE PARK, N.C. — A new research supplement published in Clinical Infectious Diseases reports findings from a multi-pathogen surveillance study in Nigeria that uncovered a wide range of previously undocumented pathogens in patients with acute febrile illness (AFI), a syndrome marked by the sudden onset of fever and other non-specific symptoms.

Led by independent scientific research institute RTI International, the Surveillance of Acute Febrile Illness Aetiologies in Nigeria (SAFIAN) study detected 20 unique pathogens, including viruses, bacteria and protozoa, many of which had not been previously documented in humans in Nigeria.

The SAFIAN study was conducted over a 12-month period in 2023–24 in partnership with Nigerian health institutions, including the University of Abuja Teaching Hospital, Irrua Specialist Teaching Hospital and APIN. Researchers enrolled 1,200 patients and used TaqMan Array Cards to screen patient specimens.  

“Using a multi-pathogen screening tool, we were able to screen each specimen for 25 different pathogens at once—something that is normally too time-consuming and expensive in routine clinical settings," said Lauren Courtney, a senior epidemiologist at RTI and the project’s principal investigator. "This approach uncovered infections that wouldn’t usually be detected, including some with global public health significance. This includes pathogens with epidemic potential, such as hemorrhagic viruses, arboviruses and certain bacteria.”

Among the pathogens detected were Yersinia pestis (plague), o’nyong’nyong virus, Bartonella spp., and Rickettsia spp. Prior to this study, the team found no documented human cases of these pathogens in Nigeria. One surprising finding was that Rickettsia spp. was detected in more SAFIAN participants than Plasmodium spp., the parasite responsible for malaria, which is endemic in Nigeria and a major focus of public health campaigns. The study also revealed that coinfections were common and often clinically indistinguishable from single infections, highlighting the diagnostic challenges of treatment of patients with non-specific symptoms.

To guide surveillance design and pathogen prioritization, the study introduced two methodological innovations, The One Health Transmission Potential Framework, developed by Claire Quiner, an infectious disease epidemiologist at RTI, assesses a pathogen’s transmission potential in a region based on its unique transmission and ecological requirements, and independent of its previous detection in a region. Pathogens deemed to have transmission potential are then fed into a second method, the Pathogen Selection tools, developed by Courtney, which weighs study objectives and other criteria to support in the final selection of pathogens to include in a given study.

RTI also provided critical capacity building for participating laboratories and clinics in Nigeria, guided by microbiologist Dr. Jean Kim. This included hands-on training, installation of specialized equipment, and rigorous quality control oversight delivered in collaboration with local partners.

The supplement includes nine peer-reviewed articles detailing the epidemiological findings, clinical characteristics and implementation strategies of the SAFIAN study. Topics range from coinfection burden and case presentations to methodologies for multi-pathogen surveillance and lessons learned.

Read the full supplement (via Clinical Infectious Diseases)

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