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Glossary · Virology

Viral variant

A strain of a virus carrying one or more mutations in its genome compared with reference strains. Most are neutral; some change transmissibility, virulence or treatment resistance.

Also called : variant, variants, variant strain, viral strain, variant viral Virology

A viral variant is a version of a virus whose genome carries one or more mutations compared with a reference strain. The vast majority of mutations are neutral and go unnoticed. A few can change transmissibility, virulence, immune escape or treatment sensitivity — only in those cases does a variant become notable. For the MV Hondius cluster, no variant of concern has been documented to date.

Mutation, variant, strain

Three levels

  • Mutation: a single change in viral DNA or RNA. RNA viruses, including hantaviruses, mutate continuously (their polymerase has a high error rate).
  • Variant: a virus carrying one or more distinctive mutations that differentiate it from a reference strain.
  • Strain: a variant sufficiently characterised and stable to be named and used as reference (for example "Sin Nombre strain", "Andes strain").

Most mutations are silent

The genetic code is redundant: several nucleotide triplets code for the same amino acid. A mutation can therefore change one nucleotide without changing the produced protein. It is then silent. Mutations that change the protein are non-synonymous; only those can potentially alter the virus's behaviour.

Variant surveillance

WHO framework

WHO classifies variants in three categories, under a framework initially developed for SARS-CoV-2 but applicable to other emerging viruses:

  • Variant of Interest (VOI): presents genetic changes likely to affect viral behaviour, without solid clinical evidence yet.
  • Variant of Concern (VOC): demonstrated impact on transmissibility, virulence, treatment efficacy or immune evasion.
  • Variant of High Consequence (VOHC): impact such that it compromises the ongoing public health strategy.

Hantavirus surveillance

Hantaviruses are relatively conserved genetically within a strain: diversity within Andes or Sin Nombre is low, unlike viruses such as SARS-CoV-2 or influenza. This facilitates detection of any atypical variant. Routine sequencing, still recent for these viruses, relies on National Reference Centres (Swiss NRZ, US NIH/CDC, French Institut Pasteur).

Application to the MV Hondius

Swiss sequencing of 5 May

On 5 May 2026, the Swiss National Reference Centre for Emerging Viral Infections (NRZ Geneva + Zurich) published on Virological.org a preliminary phylogenetic analysis of Andes virus sequences from the MV Hondius cluster. Main findings:

  • the strain is close to the Epuyén outbreak strain (Argentina, 2018-2019),
  • no unusual mutation has been documented,
  • the analysis covers the first samples; complete sequencing of all cases is in progress.

Precautionary hypothesis of 12 May

On 12 May 2026 at 17:54, Prof. Xavier Lescure (infectious disease specialist, Bichat AP-HP) raised in a press conference the hypothesis of a possible variant that may have mutated, to explain the severity of forms observed in the French patient and several foreign cases. This hypothesis was presented as precautionary, pending complete sequencing, and is not confirmed by the Swiss data of 5 May. Media coverage has sometimes turned this hypothesis into a statement of fact, which it is not.

Limits and reading caveats

Do not confuse hypothesis and confirmation

Until exhaustive sequencing has compared the genomes of all cases, the variant hypothesis remains open but unproven. Health authorities (WHO, ECDC, Santé publique France) communicate cautiously on this point.

No variant ≠ no severity

Absence of a variant does not exclude severe disease. The "ordinary" Andes virus has historically a high case-fatality rate (~30-40 %) in hospitalised patients. The severity observed in the MV Hondius cluster can be explained by host factors (age, comorbidities), high viral load, or simply the intrinsic nature of the virus, without necessarily involving a variant.

Key figures

Standards & references

Frequently asked questions

What is a viral variant?

A variant is a version of a virus whose genome carries one or more mutations (nucleotide changes) compared with a reference strain. The majority of mutations are neutral and do not affect the virus's behaviour. A minority can change transmissibility, virulence, immune escape or treatment resistance. A variant is only notable if it has a measurable phenotypic impact.

What is the difference between mutation, variant and strain?

A mutation is a single change in the genetic sequence. A variant is a virus carrying one or more distinctive mutations. A strain is a variant well-characterised and stable enough to be named and used as reference — for example Sin Nombre (North America) and Andes (Patagonia) are two hantavirus strains, while the Epuyén 2018 and Coyhaique 1997 outbreaks are two intra-strain variants of Andes.

How do we know if a variant is more dangerous?

Several parameters are evaluated in parallel: sequencing to identify mutations, epidemiological studies to compare transmissibility and lethality between cohorts, in vitro studies to test antibody and treatment sensitivity, animal studies for virulence. WHO and ECDC coordinate the assessment and publish risk briefs. A variant is never classified 'of concern' based on the sequence alone — a body of evidence is needed.

Is the MV Hondius Andes virus a variant?

The complete sequencing published on 5 May 2026 by the Swiss National Reference Centre shows that the MV Hondius strain is genetically very close to the Epuyén outbreak (Argentina, 2018-2019) and presents no unusual mutation. On 12 May 2026, Prof. Xavier Lescure (Bichat) raised, in a precautionary manner, the hypothesis of a possible variant to explain the severity of the observed forms — but this hypothesis is not confirmed by available data. Exhaustive sequencing of all cases is in progress.

Further reading