When One Introduction Becomes Two: Germany’s Shamonda Viruses Are Becoming a Test of Emerging-Disease Surveillance

A month ago, Germany appeared to be dealing with the introduction of a previously unfamiliar Shamonda-related orthobunyavirus. The situation is now considerably more complicated.

Sequence analysis by Germany’s Friedrich-Loeffler-Institut (FLI) has identified a second, substantially different Shamonda-related virus in cattle from north-western and eastern Germany. The original virus, which has circulated principally in southern Germany, Switzerland and France since July, has now been designated Shamonda virus Europe 1 (SHAV-EU1). The newly identified virus has been designated Shamonda virus Europe 2 (SHAV-EU2).

Crucially, this does not appear simply to represent continued spread and mutation of the first introduction. FLI’s initial analysis indicates that all three genome segments of SHAV-EU2 differ from those of SHAV-EU1, and the institute therefore concludes that the current situation involves two independent introduction and spread events, which are already geographically overlapping in parts of Germany.

That changes the surveillance question. Germany is no longer simply asking how far an introduced virus has spread. It must increasingly ask what exactly has been introduced, how many times it has happened, which animals are susceptible, how the viruses interact immunologically, and what happens when several related segmented viruses circulate in the same animal populations at the same time. This is what emerging-disease surveillance actually looks like — the first detection rarely provides the complete story.

From one unfamiliar virus to two

The first indication came during the summer. In July 2026, cattle in southern Germany, Switzerland and France began experiencing disease associated with a previously uncharacterised orthobunyavirus. On 3 August, FLI announced that analysis of samples from affected cattle in southern Germany had identified a virus belonging to the Simbu serogroup, with genomic analysis showing the closest relationship across all three genome segments to Shamonda virus, an orthobunyavirus historically identified in Africa and Japan.

This was significant. Simbu-serogroup viruses are predominantly associated with Africa, Asia and Australia, transmitted principally by blood-feeding Culicoides midges, and commonly infect ruminants. Europe, however, has encountered this viral group before: in 2011, another previously unfamiliar Simbu-serogroup orthobunyavirus appeared near the German-Dutch border. It became known as Schmallenberg virus, subsequently spread across large areas of Europe, and is now considered enzootic. The arrival of a Shamonda-related virus in 2026 therefore immediately attracted veterinary attention. But sequencing has now shown that Europe was apparently not dealing with one introduction. There were at least two.

The genome changed the epidemiological story

SHAV-EU2 was identified through sequence analysis of PCR-positive cattle samples originating from North Rhine-Westphalia, Lower Saxony, Hesse and Thuringia. These sequences differ substantially from SHAV-EU1: FLI reports that initial analysis shows differences across all three genome segments — orthobunyaviruses possess a segmented, negative-sense RNA genome comprising three segments generally described as L (large), M (medium) and S (small). If SHAV-EU2 were simply a descendant of the virus already circulating elsewhere in Germany, we would expect its genome to fit within that transmission and evolutionary history. Instead, the degree of genomic difference led FLI to conclude that the two viruses represent independent introduction events.

Genomic surveillance has therefore done more than identify a pathogen. It has changed our understanding of the event itself: what initially looked like a single introduction followed by spread now looks more like two separate introductions, each followed by its own spread, now geographically overlapping. That is a substantially different biosecurity problem.

We still do not know where the second virus came from

The genomic evidence supports separate introductions. It does not yet explain the pathway by which SHAV-EU2 entered Germany — more detailed phylogenetic analysis is under way. That distinction is important: a genomic difference can tell us that two viruses are unlikely to represent a single continuous transmission chain, but it cannot automatically tell us where the second virus originated, how it entered Europe, when it arrived, or which vector or movement pathway was responsible. Those questions require genomic evidence to be combined with epidemiology, vector ecology, animal movements and geographical surveillance.

The discovery therefore reduces one form of uncertainty while creating several new questions. That is normal in emerging-disease investigation. Good surveillance does not always make the situation simpler; sometimes it reveals that the situation was more complicated than we realised.

The host range is still changing

There is another uncertainty. So far, all confirmed SHAV-EU2-positive samples reported by FLI have come from cattle. SHAV-EU1 has already demonstrated a broader host range, with FLI confirming infections in cattle, horses, sheep and goats, and a positive alpaca also reported during the wider Shamonda-related virus investigation. This does not establish that SHAV-EU2 will necessarily behave in the same way; its precise host range remains unknown.

That matters both epidemiologically and operationally. A virus restricted largely to cattle creates one surveillance problem. A virus capable of circulating across cattle, sheep, goats, equids and other susceptible animals creates another. Host range affects where surveillance should occur, which clinical signs veterinarians should investigate, which populations contribute to virus circulation, and how widely exposure may already have occurred. At present, those boundaries are still being discovered.

The pregnancy question may matter more than the acute disease

In adult cattle, the clinical picture associated with these viruses can appear relatively modest: reported signs include fever, diarrhoea, reduced milk production and relatively short-lived illness. That could make the event appear economically and clinically limited. But the experience with Schmallenberg virus provides an important warning: when susceptible pregnant ruminants become infected with Schmallenberg virus during particular stages of gestation, fetal infection can cause severe congenital abnormalities, premature birth, stillbirth or abortion.

For the newly introduced Shamonda-related viruses, the extent of comparable reproductive effects is not yet clear. FLI therefore recommends particular attention to abortions, stillbirths and malformed calves or lambs originating from potentially affected herds. This creates an uncomfortable feature of the current surveillance problem: some of the most consequential effects of infections occurring today may only become apparent later in pregnancy, so the epidemiological picture in September may not reveal the full biological consequences of transmission during the summer. Surveillance needs to persist after the obvious acute wave has passed.

Then there is the immunity question

The existence of two independently introduced variants creates another important uncertainty: does infection with one protect against the other? FLI says further investigation is required to determine whether sufficient cross-protection exists between SHAV-EU1 and SHAV-EU2. If exposure to SHAV-EU1 provides strong protection against SHAV-EU2, the epidemiology of overlapping circulation could look very different from a situation in which immunity is weak or incomplete. Without knowing the answer, it is difficult to infer susceptibility simply from previous infection. Again, this is a reminder that identifying the pathogen is only the first stage — surveillance has to evolve into characterisation.

Three related viruses are now circulating

The situation becomes still more interesting when Schmallenberg virus is added. Germany now has three related Simbu-serogroup orthobunyaviruses in circulation: Schmallenberg virus, SHAV-EU1 and SHAV-EU2. This matters because orthobunyaviruses have segmented genomes, and when sufficiently related segmented viruses infect the same cell, there is the possibility that genome segments can be exchanged during replication — a process known as reassortment. FLI specifically notes that with three viruses now circulating in Germany, exchange of genome segments and resulting viral change is considered possible or likely enough to warrant attention.

That statement needs to be interpreted carefully. It does not mean a dangerous new reassortant has emerged, it does not mean one inevitably will, and reassortment does not automatically produce a virus with greater virulence, transmissibility or host range. But co-circulation creates an evolutionary opportunity that did not exist when only one virus was present, which is itself a reason for continued genomic surveillance. The question is no longer simply where these viruses are. It is also whether they are changing.

Surveillance is now watching evolution as well as geography

This illustrates why genomic surveillance becomes particularly valuable during events involving segmented RNA viruses. PCR can establish that viral material is present. Sequencing can tell us much more: it can distinguish introductions, reconstruct relationships between viruses, detect changes in individual genome segments, and potentially identify reassortment if genome segments show different evolutionary histories. The surveillance architecture therefore runs from clinical observation, through sample collection, PCR detection, whole-genome sequencing and phylogenetic analysis, to introduction identification, host-range investigation, geographical surveillance, reassortment monitoring and risk assessment. The sequence is not the end of the investigation. It changes which questions need to be asked next.

But Germany has a surveillance visibility problem

There is another important feature of the current event. Shamonda-related virus infection is not currently subject to mandatory animal-disease reporting in Germany, and FLI has explicitly acknowledged the consequence: cases are not being recorded in a precise, standardised national reporting system in the same way as notifiable animal diseases, which means FLI cannot currently generate the kind of confirmed national distribution map that would normally be derived from cases submitted by state veterinary authorities through Germany’s official animal-disease reporting infrastructure.

This does not mean Germany is not conducting surveillance — laboratories, veterinary authorities and researchers are clearly investigating the event actively. But it does mean the denominator is uncertain. We do not necessarily know how many farms are affected, how systematically animals are being tested, how comparable reporting is between regions, or how much undetected circulation exists between confirmed cases. That matters when attempting to understand the scale and direction of an emerging disease.

When should surveillance escalate?

This raises a broader One Health Security question: at what point should an unfamiliar biological event trigger a change in surveillance status? Not every newly detected virus should immediately become a nationally notifiable disease — mandatory reporting imposes costs, consuming veterinary, laboratory and administrative capacity, and many emerging detections never become significant threats. But the Shamonda event now contains several features relevant to escalation decisions: two independent introductions, continued geographical spread, multiple affected animal species, vector-borne transmission, uncertain reproductive consequences, uncertain cross-protection, and co-circulation with related segmented viruses capable of reassortment.

That does not automatically tell policymakers what the appropriate reporting status should be. It does suggest the question deserves active review. Surveillance systems need mechanisms for moving between routine observation and enhanced surveillance as the evidence changes — otherwise, the institutional response can remain fixed while the biological situation evolves.

The vector makes borders particularly porous

Culicoides midges add another dimension. These tiny blood-feeding insects are already well-established vectors of important livestock viruses, including bluetongue and Schmallenberg virus, and vector-borne disease creates a different biosecurity problem from diseases controlled primarily through direct animal movements. Farm boundaries do not stop midges. Administrative borders do not stop midges. National borders do not necessarily stop midges, and wind-assisted dispersal can move small insects considerable distances. That means surveillance cannot focus exclusively on infected animals — it also needs to understand vector activity, seasonality, weather, temperature, landscape and susceptible animal populations. This is why vector-borne animal disease sits naturally within a One Health framework even where the virus itself is not considered an important zoonotic threat. The relevant system is ecological as well as veterinary.

This is One Health without a human outbreak

There is sometimes a tendency to treat “One Health” as synonymous with zoonotic infection. That is too narrow. FLI states that viruses of the Simbu serogroup are generally not considered zoonotic pathogens and, based on current knowledge, these Shamonda-related viruses do not represent a relevant infection risk to humans. That does not make this event irrelevant to One Health — the consequences potentially extend across animal health, livestock production, farm economics, vector ecology, climate and seasonality, veterinary surveillance and food-system resilience. One Health is useful precisely because biological systems do not organise themselves according to ministerial portfolios. An emerging livestock virus does not need to infect people before it becomes a security concern.

There is an economics-of-prevention question here too

The immediate response to this event is largely an investment in information. PCR testing costs money. Sequencing costs money. Phylogenetic analysis costs money. Veterinary investigation, vector surveillance, and monitoring abortions and congenital abnormalities all cost money. Yet much of the value generated by those activities is intangible. Sequencing has already told Germany that it is dealing with two introductions rather than one; further investigation may establish whether the variants cross-protect; surveillance may determine whether SHAV-EU2 infects additional species; genomic monitoring may identify whether reassortment occurs; and reproductive surveillance may establish whether infection produces congenital disease. Each answer reduces uncertainty, and that has value because better information changes decisions.

The prevention pathway might therefore be represented as surveillance investment leading to earlier detection, better pathogen characterisation and reduced uncertainty, which in turn support better-targeted veterinary decisions and potential animal-health and production losses avoided. The difficult economic question, as we explore in our companion piece on veterinary medicine and market incentives and in our forthcoming Economics of Prevention review, is how to value that final step. If surveillance identifies a risk early and the worst outcome never occurs, the benefit is largely counterfactual — exactly the kind of problem prevention economics needs to become better at describing.

The lesson from Schmallenberg is not that history will repeat

The obvious historical comparison is Schmallenberg virus, but it needs to be used carefully. Schmallenberg emerged in Germany in 2011, spread rapidly through Europe and subsequently became enzootic. That does not mean SHAV-EU1 or SHAV-EU2 will follow the same trajectory. It does mean Europe has previous experience of how quickly an unfamiliar Culicoides-borne Simbu-serogroup virus can alter the animal-health landscape. The lesson from 2011 is therefore not that Shamonda will become another Schmallenberg. The lesson is that new vector-borne animal viruses can establish and spread before their epidemiology is completely understood — which makes the quality and speed of surveillance during the uncertain early period particularly important.

Emergence is a process, not an announcement

Perhaps the most useful lesson from Germany is how quickly the scientific description of an emerging event can change. In early August, a new Shamonda-related virus had been detected. By the end of August, multiple animal species were involved. By early September, there were two genetically distinct variants representing separate introduction events. Now, those introductions overlap geographically while a related segmented orthobunyavirus already circulates in the same country, and several fundamental questions remain unanswered: what is the origin of SHAV-EU2, how widely has it spread, what is its full host range, does infection during pregnancy cause fetal disease, does infection with one European Shamonda variant protect against the other, and will reassortment occur and, if so, will it have any biological significance?

Those are not signs that surveillance has failed. They are the questions surveillance has revealed. Emerging-disease preparedness therefore requires something more than the ability to detect a pathogen once. It requires a system capable of continuously revising its understanding as the biology changes. Germany thought it had one introduction. Sequencing showed it had two. The next discovery may change the picture again. That is why surveillance is not simply about finding threats. It is about keeping pace with them.

Questions & Answers

References

1. Friedrich-Loeffler-Institut (2026). FLI bestätigt weiteres Shamonda-Virus-verwandtes Orthobunyavirus in Deutschland. September 2026.
2. Friedrich-Loeffler-Institut (2026). FLI detects a new orthobunyavirus of the Simbu serogroup (“Shamonda-like”) in cattle in Germany. 3 August 2026.
3. Friedrich-Loeffler-Institut (2026). Shamonda virus: Newly introduced cattle virus continues to spread.
4. Friedrich-Loeffler-Institut. Shamonda virus — animal disease situation.
5. Institute of Virology and Immunology, Switzerland (2026). New orthobunyavirus of the Simbu serogroup discovered in cattle.