Utilization of Oxford Nanopore Technology for Human Infectious Diseases Detection and Surveillance in Africa: A Scoping Review

Background: Nanopore‐based sequencing by Oxford Nanopore Technologies (ONT) offers rapid, cost‐effective, and portable sequencing. As an emerging technology, ONT must be evaluated for efficacy and practical application in both high‐ and low‐resource settings. This scoping review (SR) aimed to: 1) describe how nanopore technology is used in Africa for surveillance and diagnosis of human infectious diseases, 2) describe how nanopore technology aids in the real-time detection of infectious pathogens in Africa, and 3) identify challenges and opportunities for utilizing nanopore technology in Africa to study infectious diseases. Methods: This SR followed the Joanna Briggs Institute Reviewer’s Manual framework for SRs. English‐language studies published from January 1, 2008, to April 30, 2024 that used ONT on human specimens collected in Africa and targeted ≥1 microbial agent were included. Searches were performed in Embase, Medline, PubMed, CINAHL, and the Cochrane Library. The protocol was publicly available on the Open Science Framework (1) prior to data collection. Two independent reviewers screened studies using Covidence, and data was extracted using a custom REDCap instrument. Descriptive statistics and data visualization were performed in Microsoft Excel. Results: 1162 studies were identified and 93 (8%) underwent full-text review. The portable MinION Mk1B was the most common ONT device (65% of studies). Eighty-eight studies analyzed specimens from a single African country. Of these, 45% were sequenced in the same country, 7% in a different African Country, 11% in a non-African country, and 32% did not specify location. Specimen types included direct patient specimens (62%) and cultured isolates (35%), or a combination of both. Blood, serum, or plasma was most common (35%), followed by naso- or oropharyngeal specimens (27%). Forty-four studies used ONT during an active infectious diseases outbreak, 25 of which studied SARS-CoV-2. Seventy-two studies used ONT for genomic surveillance of infectious pathogens or antibiotic resistance genes, and one study used ONT for a direct clinical application. African-affiliated authors were included as first, middle, and last authors in 46% of studies, and 15% were published by entirely African-affiliated teams. Ten studies published information on workflow timeline and five studies published the per-specimen cost. Conclusions: ONT can enable timely and affordable sequencing in African countries as demonstrated through a small number of studies that accomplished these goals individually. Improved reporting of ONT-specific methodology is needed, including timelines, cost, barcoding, flow cell model, and the use of negative controls. Publications that provide these details will enhance reproducibility and support the development of new studies using ONT for the diagnosis and surveillance of infectious diseases in low resource settings.