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Managing Infectious Disease Outbreaks Through Rapid Pathogen Genome Sequencing

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Managing Infectious Disease Outbreaks Through Rapid Pathogen Genome Sequencing BRIEFING PAPER Managing infectious disease outbreaks through rapid pathogen genome sequencing February 2021 oxfordnanoporetech.com 1 Introduction With over two million attributed deaths to Global health security depends on the rapid potential association of novel pathogen variants recognition and containment of infectious diseases (such as the COVID-19 B1.1.7 and B1.351 variants date and a projected economic cost of and no government can afford to be complacent originally identified in the UK and South Africa) with $28 trillion1, the COVID-19 pandemic has about the risks posed to population health, changes to disease severity, transmission, and economic, political, and social stability and diagnostic and therapeutic efficacy. refocused global attention on the acute, wellbeing. It is possible to be prepared to prevent ever-present threat of infectious disease. and control such threats by investing in intelligent This briefing paper describes when, where, and how and agile public health tools to monitor for potential genomic epidemiology can offer critical and timely risks, enabling responses at appropriate speed and insights for infectious disease experts, public health scale to problems as they appear. professionals, and policy-makers to stay a step ahead of infectious disease threats, responding with Executive summary Genomic epidemiology is a crucial weapon in the maximal effect. public health fight against infectious diseases, • The threat of infectious disease is ever present — providing rapid identification and complete This briefing paper is published by Oxford caused by seasonal and novel viruses, bacteria, characterisation of infectious disease pathogens. Nanopore Technologies. Our low-cost, scalable and fungi — and further compounded by growing As evidenced by the COVID-19 pandemic, genomic genomic sequencing devices have been used antimicrobial resistance epidemiology further supports precise tracking of extensively to rapidly characterise pathogens and pathogen evolution, providing detailed insights into track outbreaks, enabling informed and decisive • Significant outbreaks are an increasing risk, driven sources of infection, routes of transmission, and the action. See page 32 for more information. by globalisation, population growth, urbanisation, and climate change • Preparedness is key to minimising the potentially devastating impacts of these outbreaks • Genomic epidemiology, powered by rapid, accessible sequencing technology, provides vital information and time savings essential for rapid disease identification and control • Investment in national and regional disease surveillance and monitoring infrastructure is critical 2 OXFORD NANOPORE TECHNOLOGIES | SEQUENCING, GENOMIC EPIDEMIOLOGY, AND INFECTIOUS DISEASE [COVID-19 is a] wake-up “ call and a dress rehearsal “ for future challenges. António Guterres, Secretary-General, United Nations2 3 The importance of managing infectious disease threats KEY MESSAGES After an epidemic has subsided, there may be Although diseases passed between humans are the longer-term local, national, and global adverse most urgent concern, infectious agents that cause • Infectious diseases are an increasing threat effects on employment, health, education, trade, disease in wild or domestic animals and plants can • Outbreaks can have devastating health and travel, and quality of life. According to the also have severe economic and environmental economic consequences International Monetary Fund (IMF), the economic impacts, and indirectly or directly harm human impact of the current COVID-19 pandemic could be health; for example, foodborne disease is a major in the region of US $28 trillion1. burden in low and middle-income countries5. Even a relatively small and well-controlled Significant new outbreaks are an ongoing risk, Preparedness is vital to minimise the damage driven by increasing globalisation, population infectious diseases can cause. Even small delays or outbreak can exacerbate existing pressures growth, urbanisation, and climate change. They may mistakes in response can have significant on healthcare systems, whilst major arise from the resurgence of historical infectious implications for public health, and modest changes diseases and the spread of antibiotic resistance, or in outcome have much wider effects. For example, outbreaks may overwhelm them. Serious the emergence of infectious diseases caused by it has been suggested that the 2003 severe acute epidemics also pose significant risks of novel infectious agents (Figure 1). Novel pathogens respiratory syndrome (SARS) outbreak would have are particularly dangerous, because of the time tripled in size had there been a delay of just one wider social and economic destabilisation. needed to understand the disease, and to develop week in applying control measures6. control measures and treatments. Dr Michael Ryan, Executive Director of the World Health Organization Examination of the relative success of New Zealand (WHO) Emergencies Programme, recently in control of the COVID-19 pandemic highlighted described constant outbreaks of serious infectious that the key elements were early, decisive reactions diseases as ‘a new normal’ for which countries need from health authorities, effective surveillance Estimated economic impacts of recent infectious disease outbreaks. to be ready4. (including genomic surveillance systems), and Data from WHO3. (US dollars) targeted testing strategies7. SARS (2003) H1N1 (2009) Ebola (2014-16) COVID-19 (2019-) 40 40-50 53 billion billion billion 4 OXFORD NANOPORE TECHNOLOGIES | SEQUENCING, GENOMIC EPIDEMIOLOGY, AND INFECTIOUS DISEASE 28trillion 2009 2019 H1N1 COVID-19 influenza A 2012 new disease (swine flu) MERS 2014 new disease EBOLA 2003 SARS 2015 new disease 2005 H5N1 Zika Avian flu Figure 1: Selected infectious disease outbreaks in the 21st century Infectious diseases are an increasing threat, for example in 2019 alone the WHO recorded over 100 outbreaks of 19 different infectious diseases, each posing a potential epidemic or pandemic threat3. 5 Understanding infectious diseases KEY MESSAGES A wide range of anti-microbial drugs are currently Given these limitations, control of all human available, though in recent years the spread of infectious diseases relies on a combination of • Effective treatments are not available for all antimicrobial resistance, especially in bacteria, has prevention wherever possible (including actions to pathogens and drug resistance is increasing reduced the effectiveness of some treatments. reduce or block transmission between people) and • Prevention of transmission is critical to Detecting antimicrobial resistance in patients with rapid suppression of outbreaks where they do managing infectious disease bacterial infections is critical to ensuring that occur, alongside the use of effective treatment effective alternative treatments can be used8 or for options, where available. To do this, insights into the • Pathogen genome sequencing is a key the identification of particularly dangerous cases biology and behaviour of the pathogens that cause technique for identifying and understanding where no current antibiotics will work, such as disease are required, and as quickly as possible; infectious organisms carbapenem-resistant infections9. Vaccination to DNA/RNA sequencing is an important tool for prevent infection is possible for certain diseases, obtaining this information. Genomic epidemiology though even then some microbes such as influenza — powered by sequencing — is an essential element virus change so quickly that new vaccinations are in the design of effective prevention and control Infectious diseases are caused by needed every year; for many disease threats, no measures. vaccines exist. pathogenic microorganisms (microbes), including viruses, bacteria, fungi, and parasites. They can cause disease of varying type and severity, and many are easily spread through close contact between people. New human pathogens often come from microbes that normally infect animals, but have also acquired the ability to infect humans. 6 OXFORD NANOPORE TECHNOLOGIES | SEQUENCING, GENOMIC EPIDEMIOLOGY, AND INFECTIOUS DISEASE Types of pathogen and exemplar diseases Viral diseases Declared a global pandemic in March 2020, COVID-19, the respiratory disease caused by SARS-CoV-2, has claimed the lives of over 2 million people to date (February 2021). Bacterial diseases Responsible for over 10,000 deaths and health care costs of $2 bn per year in the US alone, methicillin-resistant Staphylococcus aureus (MRSA) is resistant to many first-line antibiotics. Fungal diseases First described in 2009 and commonly acquired in hospitals, Candida auris is associated with high mortality rate if detected late. Some strains are resistant to all three available classes of antifungals. Parasitic diseases Transmitted by infected mosquitoes, Plasmodium falciparum is the predominant cause of malaria, which results in over 400,000 deaths per year. 7 What is genomic epidemiology? KEY MESSAGES Epidemiology is the study of who develops disease, The rapid development of genome sequencing and why. Understanding how diseases occur and technologies has enabled the use genomic • Genomic epidemiology provides the detailed spread in different groups of people, including which epidemiology for infectious disease control — insights required to prevent and manage people are at greater risk, helps plan strategies to combining genomic data from pathogens with infectious disease outbreaks prevent and manage them.
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