What You’re Missing Matters: Summit India 2026

Recent viral outbreaks in many areas of the World is an important reminder of the difficulties of predicting when and where the next outbreak will occur. These also highlight the need to greatly expand our ability to rapidly identify and stop these threats. The 2013-16 Ebola outbreak took many months to detect, and it expanded in part due to the lack of local diagnosis. Similarly, despite regular disease outbreaks by known agents in many places in the world, many more viruses (known and unknown) are cryptically circulating and undetected.

Infectious diseases are often characterized by fever, and are among the most common causes of morbidity and mortality in tropical developing countries. They have devastating burden on the African continent, because differentiating the causative agents of fevers are challenging. Advances in genomic technologies have revolutionized biomedical research, and created the potential to transform the clinical care, surveillance, and understanding of infectious diseases.

Researchers at the African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s university, Ede, Nigeria, are translating microbial genomics knowledge and technologies into new field deployable diagnostics tools that can rapidly test for a wide array of known and novel microbes simultaneously. These tools are helping local health workers to perform diagnosis and treatment of patients by the patients’ bedsides and prevent outbreaks from escalating. These new developments lay the groundwork to pursue key scientific questions about the pathophysiology, epidemiology, transmission, evolution, and biology of the microbes causing disease.

In this presentation, we provide insights into how we are using new genomic knowledge and technologies to: 1) build Africa capacity and leadership toward preparedness and containment of future infectious diseases outbreaks;2) promote state-of-the-art genome sequencing and field-deployable genetic tools for microbial infections detection in West Africa, and 3) enable a surveillance network for some of the world’s greatest global health threats.

Rare genetic disorders continue to be a cause of illness and death in children in India but getting fast cheap genetic tests is hard. This talk describes the goals and results of the national Mission program for genetic disorders in children. It also explains how these goals match with the DBT-UMMID initiative to improve medicine all over the country. The Mission program has made it possible for about 3,000 families to get exome sequencing. This has led to finding 10 genes linked to diseases. It has also given families answers that help with their medical care planning and talking with counselors. A major part of the work has been checking out changes in genes that clinicians are not sure about. We use computer predictions looking at how the genes pass through families and do laboratory tests to understand these changes better and make sure the answers are right. We also are making efforts to teach doctors, patients and people in charge how to recognize rare diseases better. These efforts help with referring patients to the higher centres and helping families who are affected. We are using Oxford Nanopore Technologies (ONT) as a way to check genetic changes. This is a choice instead of Sanger sequencing because it is easier to use, gives results quickly and costs less. The small size of the machines, ability to get results quickly and the lower cost make ONT good for institutes that don’t have a lot of resources. We are making a plan to create tests for parents before they have children. These tests will use ONT to find genetic problems in different parts of India. These tests can help find out if a person carries a gene for a disease. This helps parents make choices when they are planning to have children. It also helps reduce the number of genetic diseases. All these steps show a way to take discoveries and put them into action. They show that genetic tests can help make sure that children, with diseases get proper care in India.

Our research primarily leverages long-read, high-throughput metagenomic shotgun sequencing to establish early warning systems for public health threats like virus and bacteria. Our earlier studies in India to directly sequence SARS-CoV-2 viral fragments from open urban drains using the Nanopore MinION platform helped during covid-19 pandemic and later. We successfully caught mutations associated with the Delta variant lineage in wastewater samples as early as December 2020—months before they were widely flagged in clinical data. In long-term surveillance tracking post-Omicron phases up to 2024, we proved that wastewater analysis could spot critical viral spikes or "silent waves" and track highly diverse recombinant clades (like XBB) well in advance before they were clinically identified in patients. We also utilize high-throughput Nanopore sequencing to map urban "resistomes"—the collection of antibiotic-resistant genes spreading through wastewater systems in Pune metro city. I shall talk about some case studies on environmental surveillance using Oxford Nanopore Technologies.

South Africa is home to rich and extraordinary indigenous biodiversity, spanning three of the world's 36 recognised biodiversity hotspots. Yet its human population carries one of the world's highest disease burdens, including an estimated 3.6 million people living with a rare disease, many of whom face years-long diagnostic odysseys with no clear answer. The Centre for Proteomic and Genomic Research (CPGR), a national multi-omic technology platform, and its hosted programme, DIPLOMICS (DIstributed PLatform in OMICS), have built the continent’s largest long-read sequencing capacity and infrastructure, enabling researchers to pursue opportunities and tackle challenges facing South Africa. Two flagship programmes run on those Nanopore platforms. 1KSA, our national biodiversity genome sequencing project, generates de novo reference assemblies for indigenous South African species, supporting conservation, agriculture and national claims to digital sequence information (DSI). Nngwe applies long-read whole-genome sequencing and multi-omics to patients with rare and undiagnosed diseases, targeting the structural and repeat variation that short reads miss. Our infrastructure model, supported by Oxford Nanopore Technologies, centralises sequencing and bioinformatics, distributes sampling and expertise, and builds a talent pipeline that keeps African data in African hands. Real challenges remain: securing sustainable funding, accessing computing resources, and assembling complex genomes de novo. The common thread is simple: what you miss matters, whether it is a species never sequenced or a variant never seen.