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Infectious disease outbreaks threaten human, animal and plant health, and they have implications for global health, food security, biodiversity and economic stability. This Collection contains articles from Nature Reviews Microbiology that explore the emergence, identification, spread, pathogenesis, impacts and management of local or global outbreaks caused by pathogens, including emerging and re-emerging viruses such as SARS-CoV-2, Ebola virus and novel influenza viruses, as well as fungi and drug-resistant bacteria. Increased knowledge of the origin and characteristics of infectious disease outbreaks are prerequisites for the successful management of current outbreaks and the prevention of future outbreaks, and thus for ensuring the planet’s health.
The integrative environment-health sciences including One Health, Conservation Medicine, EcoHealth and Planetary Health embody the transdisciplinary synthesis needed to understand the multitude of factors that underpin emerging infections and their management. Future successes in confronting and resolving the complex causal basis of disease emergence to generate robust, systems-oriented risk reduction strategies that preserve both human health as well as promoting sustainable futures represent the ‘Moon Shot’ for the integrative environment-health sciences.
In this Review, Shi and colleagues summarize the exceptional amount of research that has characterized acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease 2019 (COVID-19) since this virus has swept around the globe. They discuss what we know so far about the emergence and virology of SARS-CoV-2 and the pathogenesis and treatment of COVID-19.
In this Perspective, Su, Du and Jiang discuss lessons from previous vaccine development efforts for other viruses and how the mechanisms of vaccine-associated disease enhancement seen in some viral infections can inform the development of a safe and efficacious COVID-19 vaccine.
The COVID-19 pandemic has prompted unparalleled progress in the development of vaccines and therapeutics in many countries, but it has also highlighted the vulnerability of resource-limited countries in Africa. Margolin and colleagues review global efforts to develop SARS-CoV-2 diagnostics, therapeutics and vaccines, with a focus on the opportunities and challenges in Africa.
Bats harbour a large number of different viruses, some of which have spilled over to cause human disease. In this Review, Letko, Munster and colleagues discuss the diversity of bat viruses and the factors that determine the emergence of zoonotic viruses from bats.
Filoviruses such as Ebola virus pose a substantial health risk to humans. Advances in genomic technologies have enabled the rapid, large-scale generation of virus sequence data at the location of disease outbreaks and thus the use of reverse functional genomics to swiftly characterize the threat of, and treatment for, filovirus disease.
Influenza A viruses cause pandemics when they cross between species. In this Review, Barclay and colleagues examine the host barriers that influenza A viruses must overcome to initiate a pandemic in humans and describe how, on crossing the species barrier, the virus mutates to establish new interactions with the human host.
Previously, Zika virus was thought to cause mild infection, and serious complications only recently emerged. Liu, Shi and Qin discuss how the virus has evolved during its recent global spread and consider how these changes might be linked to pathogenesis.
In this Review, Weaver and colleagues discuss the role of genetic drift following population bottlenecks and founder effects in mosquito-borne arboviral evolution and spread, and the emergence of human disease, focusing on chikungunya virus and Zika virus.
Over the past decade, Klebsiella pneumoniae has emerged as a major clinical and public health threat. In this Review, Wyres, Lam and Holt discuss how genomics approaches have advanced our understanding of K. pneumoniae taxonomy, ecology and evolution as well as the diversity and distribution of clinically relevant determinants of pathogenicity and antimicrobial resistance.
Meningococcal disease remains an important cause of morbidity and death worldwide despite the development and increasing implementation of effective vaccines. In this Review, Caugant and Brynildsrud discuss how high-throughput sequencing approaches have advanced our understanding of the diversity and evolution of Neisseria meningitidis and the pathogenesis of N. meningitidis infection and how they are helping to explain the epidemiology of meningococcal disease.
Non-tuberculous mycobacteria, such as Mycobacterium abscessus, are an increasing global health burden, in part due their extensive drug resistance. In this Review, Johansen, Herrmann and Kremer discuss the infection process, host interactions, mechanisms of drug resistance and drug development.
Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen both within hospitals and in the community. In this Review, Fowler and colleagues provide an overview of basic and clinical MRSA research and explore the epidemiology, transmission, genetic diversity, evolution, surveillance and treatment of MRSA.
In this Review, Jones and colleagues describe the extremely diverse Xanthomonas spp. and how these plant pathogens use their extensive repertoire of effectors for virulence and immune evasion. Understanding these prototypical plant pathogens paves the way to combat disease.
Worldwide amphibian declines caused by pathogenic chytrid fungi are emblematic of the emerging infectious diseases driven by globalization. Fisher and Garner discuss how these wildlife pathogens emerge to drive global declines in amphibian biodiversity and the implications of current research for policy and control measures.
The fungal pathogen Pseudogymnoascus destructans, which causes white-nose syndrome in bats, has devastated bat populations in North America since its introduction from Eurasia in the 2000s. In this Review, Hoyt and colleagues describe the ecology of P. destructans in bats and its impacts on bats and the ecosystem.