Unofficial site — data consolidated from public sources (WHO, ECDC, CDC, French health authorities, verified press). View sources.

Glossary · Diagnostic

Genetic sequencing

Determining the exact nucleotide order of a viral genome. Used to identify variants, retrace transmission chains and compare strains.

Also called : genome sequencing, whole-genome sequencing, WGS, next-generation sequencing, NGS, Sanger sequencing, séquençage génétique Diagnostic

Genetic sequencing determines the exact order of nucleotides — A, T (or U for RNA), G and C — that make up a viral genome. For hantaviruses, sequencing makes it possible to distinguish one strain from another, compare viruses sampled from different patients, and detect any mutations associated with a change in viral behaviour. The MV Hondius cluster was sequenced for the first time on 5 May 2026 by the Swiss National Reference Centre.

Technical principle

From genome to sequence

All RNA viruses, including Andes virus, carry their genetic information in one or more RNA strands. For hantaviruses, the genome is tri-segmented:

  • S segment (~1.8 kb) — encodes the nucleoprotein,
  • M segment (~3.6 kb) — encodes the envelope glycoproteins Gn and Gc,
  • L segment (~6.4 kb) — encodes the viral RNA polymerase.

Sequencing produces a chain of letters representing the exact order of each nucleotide. A complete hantavirus sequence contains about 11.8 kilobases (kb).

Technologies

Three main families coexist:

  • Sanger: historic technology (1977), accurate but slow. Still used to verify short fragments.
  • Illumina (NGS short-read): high throughput, short reads (~150 nt), requires bio-informatics assembly.
  • Oxford Nanopore (NGS long-read): long reads (several kb), portable, ideal for field deployment and real-time surveillance.

For hantaviruses, reference labs generally combine Illumina (accuracy) and Nanopore (speed). Turnaround from RNA extraction to a complete sequence is 24-72 hours on modern platforms.

Application to the MV Hondius cluster

First sequence — 5 May 2026

The Swiss National Reference Centre for Emerging Viral Infections (NRZ Emerging Viruses, Geneva University Hospitals + Institute of Medical Virology, University of Zurich) published the first phylogenetic analysis of Andes virus sequences from the MV Hondius cluster on Virological.org, on 5 May 2026.

Main findings:

  • the strain is genetically very close to the Epuyén outbreak (Argentina, 2018-2019);
  • no unusual mutation has been documented, including in the envelope glycoprotein genes (M segment) involved in transmissibility;
  • the analysis covers the first samples; exhaustive sequencing of all cases is in progress.

Variant hypothesis — 12 May 2026

On 12 May 2026 at 17:54, Prof. Xavier Lescure (infectious disease specialist, Bichat AP-HP) raised in a press conference the precautionary hypothesis that a possible "variant that may have mutated" could explain the severity of forms observed in the cluster. This hypothesis is not confirmed by the Swiss data of 5 May, which on the contrary show high genetic proximity to known Argentinian strains. Exhaustive sequencing of all cases is expected to settle the question.

Molecular surveillance

Phylogeny

Published sequences are deposited in public banks (GenBank, NCBI) and analysed with tools such as Nextstrain, which build the virus's phylogenetic tree. These trees show which strains are related, when they diverged, and thus retrace transmission chains.

Variant detection

Nucleotide changes (mutations) are common in RNA viruses, and most are silent or neutral. Particular attention is paid to mutations in:

  • the envelope glycoproteins (M segment): transmissibility and immune recognition,
  • the polymerase (L segment): antiviral resistance,
  • the nucleoprotein (S segment): major antigen, target of serological tests.

Further considerations

Complete cluster sequencing also makes it possible to date approximately the virus's introduction into a population (molecular clock), estimate diversity within the cluster, and compare the identified strain to all known global strains via GenBank. For hantaviruses, it is the only way to formally distinguish intra-cluster transmission from multiple introductions from animal reservoirs.

Key figures

Standards & references

Frequently asked questions

Why sequence a virus?

Sequencing answers three key questions: identify precisely the viral species and strain (beyond what PCR tells), compare viruses sampled from different patients to reconstruct transmission chains, and detect any mutations associated with a change in transmissibility, virulence or treatment resistance. It is the reference tool for molecular outbreak surveillance.

How long does complete sequencing take?

With modern platforms (Illumina, Oxford Nanopore), complete sequencing of a small viral genome like hantavirus (~12 kb) can be obtained in 24 to 72 hours from sample. The pipeline includes viral RNA extraction, targeted amplification, library preparation, NGS run and bio-informatics analysis. For the MV Hondius cluster, the first complete sequence was published on 5 May 2026, about 48 hours after the first PCR positives of 3 May.

What do we know about the MV Hondius Andes sequence?

The sequencing published on 5 May 2026 by the Swiss National Reference Centre for Emerging Viral Infections (NRZ, Geneva + Zurich) shows that the MV Hondius strain is genetically very close to the Epuyén outbreak strain (Argentina, 2018-2019). No unusual mutation has been documented at this stage. On 12 May 2026, Prof. Xavier Lescure (Bichat) raised the precautionary hypothesis of a possible variant, pending full sequencing of all cases — this hypothesis is not confirmed by the Swiss data of 5 May.

What is the difference between sequencing and PCR?

PCR detects the presence of a target RNA or DNA fragment: it answers 'is the virus there?'. Sequencing determines the exact sequence of the viral genome: it answers 'which virus, precisely?'. PCR is fast (a few hours), inexpensive, and the frontline diagnostic tool. Sequencing is slower and more expensive, but produces much richer information, essential for molecular surveillance and epidemiology.

Further reading