Genomic evidence confirms natural evolution (variance) of Andes hantavirus

It's not a new strain (according to sequencing data)

A Swiss passenger (case 7, ANDV/Switzerland/Hu-3337/2026) was infected aboard the MV Hondius cruise ship during its voyage that began on April 1, 2026, from Ushuaia, Argentina.

Dr. Steven Quay reported on X

Dr Steven Quay@quay_dr

BREAKING: First sequencing of the Hantavirus from the outbreak. -99% identical to a June 2018 case from a patient in Argentina -10.4 SNV/year mutation rate - The Andes genome is about 12 kb across three RNA segments. At 10⁻⁴ to 10⁻³ substitutions/site/year, that translates

11:31 AM · May 11, 2026 · 274K Views

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the first sequencing of Andes hantavirus from the ongoing outbreak, showing approximately 99% identity (rounded) to a June 2018 human case from Argentina with an observed ~10.4 SNV/year mutation rate consistent with natural RNA virus evolution. The ~12 kb genome across three RNA segments exhibits substitution rates (roughly 1-12 SNVs/year) matching expected rodent-host spillover dynamics, placing the 2026 strain’s divergence in line with eight years of natural circulation.

Here’s the fasta file.

Andv Switzerland Hu 3337 2026

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The virus has been sequenced from this person and the strain does indeed show approximately 98.7% identity (98.71–98.76% depending on segment) with 100% query coverage to Orthohantavirus andesense isolate NRC-4/18_06/01/2018 segment L, complete sequence (ACCESSION #: MN258159; VERSION: MN258159.1), as confirmed by me. This is the L segment of Andes virus (Orthohantavirus andesense) isolate NRC-4/18, collected on June 1, 2018, from a human patient in San Martín de los Andes, Neuquén Province, Argentina.

You can click the photos to go to the BLAST data.

So this strain is a descendant of the known circulating strain in the Argentina region, consistent with natural evolution in rodent reservoirs and occasional human spillovers. This is standard for RNA viruses - they accumulate mutations steadily but don’t reinvent themselves overnight. The current outbreak strain behaves like known ANDV: rodent spillover (likely originating in/near Ushuaia, Argentina, via the index case or closely related events), with limited person-to-person transmission in close quarters (e.g., the cruise ship).

Interestingly, this work was a direct GenBank submission on July 29, 2019, with collaboration from the Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases (USAMRIID), but the primary paper is marked as unpublished. USAMRIID contributed to the Illumina sequencing (and…?).

The sequencing technology is explicitly listed as Illumina in the assembly metadata for the related segments (e.g., MN258226 for the S segment). The assembly/processing tools were cutadapt, Prinseq-lite, Picard, Bowtie2, and Ray - standard for processing Illumina short-read data. Minimum coverage was variable (at least 3X).

The work was carried out primarily in the Martinez Lab by Valeria P. Martinez’s group (Argentina’s national hantavirus reference lab). They routinely employ next-generation sequencing (NGS), including Illumina platforms (e.g., MiSeq), often with targeted enrichment, amplicon-based, or bait-capture methods for Andes virus genomes. This aligns with their workflows for other 2018-era strains and later outbreaks.

This was standard public health surveillance sequencing in 2018–2019 - high-throughput short-read Illumina NGS. The resulting reference genomes have been widely used since deposition. There are no indications of unusual or non-standard methods for this isolate.

Take-home message

This is not a “new strain” and the sequencing data strongly indicate we are not looking at gain-of-function work or recent engineering. At least, not unless the 2018 Argentine patient was the subject of a GOF experiment back in the day.