Drivers of Emergence, Spillover and One Health

A virus is called emerging when it is newly recognised in a host species, or when a known virus expands into a new geographical area or a new host, often with a change in how much disease it causes. The defining fact about emerging viruses is where they come from. Of roughly 1,400 recognised human pathogens, more than half originated in animals, and more than 300 pathogens were recognised as having emerged between 1940 and 2004, a period of rapid change in agriculture and urbanisation. Viruses are heavily over-represented in this group, and the central question of the field is not only which virus will emerge next but what forces push any virus across the barriers that normally separate it from us. Those forces are mostly ecological and social rather than viral, which is why emergence is best understood as a property of the changing relationship between virus, host and environment, not of the virus alone.

What “emerging” and “re-emerging” mean

An emerging infection has three recognisable forms: a genuinely new or previously unrecognised agent, a known agent moving into a new ecological niche or geographical zone, and an existing agent that has shifted in pathogenicity. The worked examples span all three. Severe acute respiratory syndrome (SARS) appeared abruptly in 2003 as a new agent; West Nile virus was long known in Africa and the Middle East before it reached New York in 1999; and Zika virus circulated for decades as a mild febrile illness in East Africa before emerging to cause major disease, including congenital malformation, in the Pacific and the Americas. A re-emerging infection is a known agent that reappears or expands, usually because a social or ecological barrier has fallen: poliovirus returning to a conflict zone, or hepatitis B spreading through new parenteral medical practices.

A perceived new disease is not always a newly circulating virus, and separating true emergence from improved recognition matters. New diagnostic tests sharpen the apparent extent of a virus that was already endemic, as happened with hepatitis B, hepatitis C, rotavirus and the human papillomaviruses. Changes in human behaviour can alter the epidemiology of an endemic virus without any change in the virus itself: improved sanitation delayed the average age of poliovirus infection into later childhood, when paralytic disease is far more common, so better hygiene paradoxically produced more visible disease. The most important principle sits underneath all of this. Although circulating viruses constantly evolve by mutation, recombination and selection, pure mutation is an uncommon route to a genuinely new human disease; most newly emerging viruses acquire their new genetic material from infections of non-human species, that is, from zoonosis. Emergence is therefore first an ecological event and only second a genetic one.

Viruses are disproportionately represented among emerging agents, and RNA viruses account for roughly one third of all emerging and re-emerging infections. The reason is evolutionary. RNA viruses combine high mutation rates, enormous population sizes, short generation times and, in segmented genomes, the capacity to reassort, so they can adapt to a new host on a timescale of days to weeks, against the years to millennia over which mammalian hosts change. The molecular machinery behind this speed is the subject of the Viral Evolution article; here it is enough to note that the same fast evolution that makes RNA viruses hard to vaccinate against and quick to resist drugs is what lets them cross species in the first place.

The drivers of emergence

Emergence is rarely the result of one factor. A genetic change in a virus usually coincides with a change in transmission or host contact, and which was cause and which was consequence often matters little. It is useful to group the drivers under the three things they act on: the virus, its transmission, and host resistance.

Acting on the virus	Acting on transmission	Acting on host resistance
Mutation and selection	Climate and weather	Immunosuppression
New genetic material from zoonosis, recombination or reassortment	Overcrowding and urbanisation	Nutritional state
	Rapid air travel and trade	Herd immunity
	Changes in sexual behaviour
	Injecting drug use
	New medical interventions
	War, famine and displacement
	Movement into new environments
	Vector density and exposure

Climate change, meaning a statistically significant shift in the mean over a prolonged period rather than short-term variation, reshapes the ranges of vectors and reservoirs. Vector-borne transmission is acutely temperature-sensitive and rises steeply, not linearly, with warming, so a small temperature change has a disproportionate effect. The mosquito Aedes aegypti, the principal urban dengue vector, is limited by the 10 degrees Celsius winter isotherm, and as that line shifts the virus reaches further from the equator. Climate cycles act over the short term too: the El Nino Southern Oscillation, a periodic shift in Pacific sea-surface temperature, drove the drought-then-rainfall sequence that triggered the 1993 emergence of hantavirus pulmonary syndrome from Sin Nombre virus in the southwestern United States, where the end of a drought produced a boom in deer-mouse numbers and a surge in human exposure.

Movement of people and goods disperses viruses faster than ever. International air travel carried SARS-CoV-2 from China to dozens of countries across the globe within the span of a few weeks, and modelling shows that the journeys an index case makes can decide whether an outbreak is containable. The trade in animals is a parallel conduit: hundreds of thousands of wild-caught animals are traded each year, each an opportunity for a reservoir virus to meet a new host, and even the vector can travel, as in the theory that West Nile virus reached New York in 1999 inside a mosquito that survived an intercontinental flight. Deforestation and movement into previously wild environments strip away the predators that keep reservoir populations in check and place people in direct contact with novel viruses, while war and the collapse of public-health programmes let controlled diseases return, as polio did in Gaza in 2024.

Underlying much of this is the oldest driver of all. Agriculture, beginning roughly 10,000 years ago, created the dense, settled human populations and the close contact with livestock and commensal animals that allowed viruses to cross into people and then persist, giving rise to the human crowd diseases. Measles is thought to have evolved from the cattle virus rinderpest once human population centres grew large enough to sustain it without an animal reservoir, and smallpox from a poxvirus of camels. The same logic explains why the highest-risk interfaces today are intensive animal farming, live-animal markets and the expanding edges of cities.

Spillover and the species barrier

Spillover is the transmission of a virus from its animal reservoir into people. Whether a spillover goes anywhere depends on what the virus can do next, and it is helpful to read emergence as a five-stage path from a virus locked in animals to one fully adapted to humans. The boundaries between stages are indistinct, and a virus can sit at any stage for a long time before moving, or never move at all.

Stage	What it describes	Transmission to humans	Examples
I	Agent present only in animals	None	Many animal viruses
II	Primary spillover	Only from animals	Rabies, West Nile virus, Hendra, H5N1 avian influenza
III	Limited human outbreak	From animals, or a few human-to-human cycles	Ebola, Marburg, mpox
IV	Sustained but reservoir-fed outbreaks	From animals, or many human cycles	Yellow fever, dengue, influenza A
V	Exclusively human agent	Only between humans	Measles, mumps, rubella, smallpox, hepatitis C

The basic reproduction number, written R0, is the average number of new infections one case produces in a fully susceptible population, and it is the key to the stages. Many zoonotic viruses cannot transmit between people at all, so their human R0 is effectively zero and every human case requires fresh exposure to the animal reservoir, as with Lassa fever in West Africa. Where some human-to-human transmission is possible, R0 approaches one, and these viruses cause the greatest concern, because a small change in the host-virus relationship, raising R0 just past one, can convert a self-limiting cluster into a sustained epidemic. A virus that completes the journey to stage V, as HIV-1 did after a small number of cross-species transfers from chimpanzees, is no longer zoonotic at all; it has cut its animal cord and is maintained entirely in people.

Crossing the species barrier takes more than contact. The virus must be able to attach to and enter cells of the new host, which usually depends on receptor compatibility, then replicate and shed efficiently enough to reach the next person, and host-adapted variants must be selected along the way. This is why successful jumps are more likely between closely related host species, which share similar cell-surface receptors and often the same habitat. The asymmetry between viral and host evolution is the deeper reason emergence happens at all: a virus can adapt to a new host almost instantly on the timescale over which the host itself evolves defences.

Reservoir and vector cycles

A few recurring roles describe how viruses are maintained in nature and reach people. The reservoir host maintains the virus long-term, usually without serious disease, and is the source from which spillover ultimately draws; bats are the reservoir for the lyssaviruses, the henipaviruses and the filoviruses, while rodents of the family Muridae host almost all the arenaviruses and hantaviruses. An amplifying or intermediate host is one in which the virus multiplies to high levels and bridges to people, the role pigs played in the Malaysian Nipah outbreak, where fruit bats infected pigs and pigs infected farmers. A dead-end host becomes infected but does not transmit onward, the position of humans and horses in West Nile virus infection, where birds are the amplifying reservoir.

For vector-borne viruses, an arthropod carries the virus between hosts, and a bridge vector is one that feeds on both the reservoir and on people, carrying the virus across from its animal cycle, as Culex mosquitoes bridge West Nile virus from birds to humans. The terms enzootic and epizootic mirror endemic and epidemic in animals: enzootic transmission is the steady background maintenance of a virus in its reservoir, while an epizootic is an outbreak in the animal population, and an epizootic frequently precedes the human cases. Many arboviruses run two linked cycles: a sylvatic (jungle) cycle that maintains the virus among forest animals and forest mosquitoes, and an urban cycle in which the virus is transmitted human to human by domestic mosquitoes such as Aedes aegypti, the pattern that lets yellow fever, dengue, Zika and chikungunya move from the forest edge into cities. The detailed group structure of the arboviruses and the rodent-borne hantaviruses is treated in their own overview articles within this topic.

Where new viruses come from

Newly identified emerging viruses almost always fall within a handful of well-characterised families, even as the wider virosphere of uncharacterised viruses is still being explored. Reading emergence by reservoir and family makes the pattern legible: a small number of animal groups, above all bats and rodents, supply most of the new human viruses, and a few RNA-virus families account for most of the serious ones.

Family (group)	Main reservoir	Emerging viruses of concern
Coronaviridae	Bats	SARS-CoV, MERS-CoV, SARS-CoV-2
Filoviridae	Bats	Ebola, Marburg
Paramyxoviridae (henipaviruses)	Fruit bats	Nipah, Hendra
Orthomyxoviridae (influenza A)	Wild birds, with pigs as a mixing host	H5N1, H7N9, pandemic H1N1
Flaviviridae	Primates, birds, mosquito cycles	Dengue, yellow fever, Zika, West Nile
Bunyavirales	Rodents, ticks	Hantaviruses, Crimean-Congo haemorrhagic fever, Rift Valley fever
Arenaviridae	Rodents	Lassa, lymphocytic choriomeningitis virus
Rhabdoviridae (lyssaviruses)	Bats, carnivores	Rabies and rabies-related lyssaviruses
Retroviridae	Non-human primates	HIV-1 and HIV-2, from simian immunodeficiency viruses
Poxviridae	Rodents	Mpox

Several of these illustrate emergence especially clearly. HIV-1 arose from at least three separate cross-species transfers of simian immunodeficiency virus, giving the M, N and O groups, each a distinct spillover from chimpanzees or gorillas, and its global spread then depended entirely on human behaviour and human-to-human transmission. The henipaviruses show the role of the amplifying host and of human encroachment: Hendra emerged when horses grazed under bat-roosting trees in Queensland, and Nipah when pig farms expanded into bat habitat in Malaysia. The filoviruses Ebola and Marburg are maintained in bats and spill into people sporadically, with the cave-roosting Egyptian fruit bat implicated for Marburg, while influenza A shows the distinctive route of reassortment, with the pig acting as a mixing vessel in which avian, human and swine influenza genes can combine, the process that produced the 2009 pandemic H1N1 from a triple-reassortant ancestor.

One Health

Because emergence happens at the interface between people, animals and the environment, it cannot be understood or prevented from within human medicine alone. One Health is an integrated approach that treats the health of people, animals, plants and ecosystems as a single interdependent system, and uses the links between them to build better surveillance and control. The approach is not abstract: the World Health Organization (WHO) estimates that more than 60% of emerging infectious diseases reported globally come from animals, and that human pressures on ecosystems, animal trade, intensive farming, urbanisation, extractive industry, deforestation and climate change, are what create the new opportunities for spillover.

One Health is now organised internationally through the Quadripartite, a partnership of the WHO, the Food and Agriculture Organization of the United Nations (FAO), the World Organisation for Animal Health (WOAH) and the United Nations Environment Programme (UNEP), which together produced a One Health Joint Plan of Action and are advised by the One Health High-Level Expert Panel (OHHLEP). Its scope reaches beyond zoonoses to antimicrobial resistance, vector-borne disease, food safety and environmental health. The economic case is strong: the World Bank has estimated that One-Health-guided pandemic prevention would cost in the region of US$10 billion per year, a modest figure against the cost of a single pandemic, which makes prevention one of the most cost-effective investments a country can make. The COVID-19 pandemic is widely read as a demonstration of what the gaps in One Health surveillance and integration can cost, and as the strongest argument for closing them.

Recognising and responding to a new agent

When a new agent appears, the priorities are to characterise it and to contain it at once. The first assessment asks where it came from, including both its viral ancestors and its likely reservoir, how it is transmitted, how lethal it is, and how transmissible it is. Control then rests on a set of standing requirements: clinicians alert enough to notice the unusual, high-standard local diagnostics backed by reference-laboratory expertise, practical case definitions for field use, isolation and infection control for cases, the early involvement of epidemiologists, and the authority and resources to act. Surveillance is the foundation of all of it, requiring a unified system that tracks both human and animal health. Exactly what happens when that integration fails has been repeatedly laid bare: first by the emergence of COVID-19 in China, and more recently by the H5N1 cattle outbreaks in the USA. The detailed machinery of outbreak investigation, surveillance systems and pandemic preparedness is the subject of the Outbreaks, Surveillance and Pandemic Preparedness article.

South African context

South Africa is a significant node in continental and global emerging-disease surveillance, and the National Institute for Communicable Diseases (NICD), part of the National Health Laboratory Service (NHLS), operates the only biosafety level 4 (BSL-4) laboratory on the African continent, within its Centre for Emerging Zoonotic and Parasitic Diseases. That centre is the national and regional reference point for the viral haemorrhagic fevers, the arthropod-borne viruses, rabies and other high-consequence pathogens, providing differential diagnosis, outbreak response and research capacity not only for South Africa but for the Southern African Development Community and the wider continent. Its position matters because the geography of emergence in this region, bat-borne filoviruses, rodent- and tick-borne haemorrhagic fevers, and a heavy arbovirus burden, demands exactly this kind of high-containment reference capability.

The institute’s role is best seen in how its surveillance modalities combine. Laboratory reference diagnosis lets it identify a rare agent quickly: when a cluster of severe respiratory illness aboard an Antarctic cruise vessel was traced to an Andes hantavirus, it was the NICD that provided the first laboratory confirmation after a passenger died on arrival in Johannesburg, alerting the wider world to the nature of the outbreak. Environmental surveillance extends the reach of conventional case-based systems: NICD wastewater testing during the South African measles outbreaks demonstrated that environmental sampling can detect viral circulation in a community and support elimination programmes, a technique that matured during the COVID-19 pandemic and is now applied across several pathogens. Outbreak response and reporting tie the system together, as in the institute’s situational reporting and continental coordination during the 2026 Ebola outbreak caused by Bundibugyo virus in the Democratic Republic of the Congo and Uganda, which the WHO declared a Public Health Emergency of International Concern. The durable point is structural rather than tied to any one event: South Africa’s value lies in a standing reference and high-containment capability, integrated zoonotic and environmental surveillance, and a coordinating role across the region.

References and recommended reading

• Burrell CJ, Howard CR, Murphy FA. Emerging Virus Diseases. In: Fenner and White’s Medical Virology, 5th edition, Chapter 15. Academic Press / Elsevier; 2017. The foundational account of emergence, drivers, spillover and zoonotic origins on which this article principally draws.
• World Health Organization. One Health. WHO fact sheet; 2026. The current reference for the One Health definition, the Quadripartite partnership and the economics of prevention.
• National Institute for Communicable Diseases. Centre for Emerging Zoonotic and Parasitic Diseases. NICD; 2026. The reference for South Africa’s high-containment and zoonotic-disease reference capacity.
• Ndlovu N, McCarthy KM, Mabasa VV, et al. Wastewater testing during the South African 2022 to 2023 measles outbreak demonstrates the potential of environmental surveillance to support measles elimination. NICD Centre for Vaccines and Immunology; 2024. The South African environmental-surveillance source.