The project “No more pandemics” aims to set a new standard for the diagnosis of infectious diseases and antimicrobial drug resistance (AMR) by ensuring access for all patients to a novel technology to test for all infectious diseases; nanopore sequencing using MinION devices.
Nanopore sequencing can be used to characterize the genetic material of micro-organisms, which helps to identify them and determine their drug resistance. In the project, evidence will be generated on the effectiveness, feasibility, acceptability, and costs of using nanopore sequencing for the diagnosis of COVID-19, (drug-resistant) tuberculosis, other infectious diseases, and antimicrobial drug resistance. In the project, KNCV, together with partners, plans to demonstrate the use of this technology in Kyrgyzstan, Tanzania, and Vietnam.
Background
In addition to the mortality caused by COVID-19, yearly more than 8 million people die from other infectious diseases, including 1.6 million deaths from tuberculosis (TB). In addition, nearly one million people die because of drug resistance in infectious diseases. Mortality from infectious diseases, especially TB, is particularly high in developing countries. The lack of a timely and correct diagnosis is an important cause for this. As a result, people sometimes do not get access to the right treatment, or they get it too late. Diagnosis of a disease is often delayed because a separate test must be done for each disease. In addition, determination of drug resistance may take a long time and is often only possible in specialized laboratories in centralized settings, which may be far from the patients.
Mortality from infectious diseases can be reduced with effective early diagnosis followed by appropriate treatment and infection control. In principle genome sequencing enables simultaneous detection of specific microbes, their epidemiological markers and drug resistance testing in a single assay. So far, this technique has been used mainly in large institutes for research and surveillance purposes in high-income countries. However, recent innovations enable genome sequencing close to the point of care at relatively low cost, for instance by nanopore sequencing using portable MinION devices (Oxford Nanopore Technologies, United Kingdom). Implementation of genome sequencing for diagnostic purposes will facilitate early and accurate diagnosis and, thus, reduction in infectious diseases morbidity and mortality. In addition, it will contribute to surveillance, preparedness, and timely response. Ultimately, near patient sequencing promises real-time collection of data about infectious diseases and their spread which could contribute to preparedness and response to prevent future pandemics.
MinION device attached to a laptop computer.
Dream Fund project ‘No more pandemics’
On April 1st 2021, KNCV started the project “No More Pandemics”, supported by the Dutch Postcode Lottery Dream Fund. In this project, the use of nanopore sequencing for the diagnosis of infectious diseases by using MinION devices will be demonstrated in low- and middle-income countries. It is innovative because, so far, this technique has been used mainly in large institutes in high-income countries for research and surveillance purposes. The project will generate evidence on the effectiveness, feasibility, acceptability, and costs of using nanopore sequencing for the diagnosis of COVID-19, (drug-resistant) tuberculosis, and other pathogens and their drug resistance patterns. Challenges and critical issues will be highlighted guiding future development and scale up.
Project countries and partners
The Laboratory for Medical Microbiology Twente-Achterhoek (Labmicta) and the National Institute for Public Health and the Environment (RIVM) in The Netherlands are partners in the project that is lead by KNCV. They support the development of protocols, training, and research. The use of the MinION will be demonstrated in Kyrgyzstan, Tanzania and Vietnam, where we collaborate with the national reference laboratories.
Group photo taken during the first training of national reference laboratory staff, December 2022.
Project approach
We will first introduce the MinION to the national tuberculosis laboratories to familiarize them with the technology and build capacity centrally. They are the ones who will support the nationwide deployment of this technology. Subsequently, we will make the MinION available to others, starting with the lung hospitals. Collaboration will also be sought with the relevant local associations of healthcare professionals, to generate support for the implementation and jointly adjust guidelines. In addition, we will disseminate project results to relevant partners and discuss the new possibilities that the MinION offers.
In the first phase of the project, we will use the nanopore sequencing for surveillance of COVID-19 and diagnostics for drug resistance in TB and scale up the implementation thereof. Subsequently, we will expand the use of nanopore sequencing for other infectious diseases. Experiences of patients and practitioners, use of the test and treatment outcomes will be closely monitored, documented, evaluated and brought to the attention of policy makers in the countries themselves and internationally.
Approach of KNCV’s Dream Fund project ‘No More Pandemics” in which the use of Nanopore sequencing (Oxford Nanopore Technologies (ONT), United Kingdom) with hand-held MinION devices for the diagnosis of infectious diseases is demonstrated in Kyrgyzstan (KGZ), Tanzania (TZA) and Vietnam (VNM).