Initial genetic analysis of the ‘MV Hondius’ hantavirus outbreak confirms it belongs to the Andes strain and rules out mutations
The sequencing was performed using material from the Swiss patient on board the cruise ship
The hantavirus from the MV Hondius outbreak has been sequenced from samples taken from one of the infected individuals. The results confirm that it is the Andes strain, the most virulent and contagious, but rule out any mutation. Sequencing the virus is now a priority for the scientific community. It holds within its structure a black box of crucial information: it can help identify how the virus spread, why so many people have become ill (to date, there are 10 suspected cases and three deaths from a virus considered very difficult to transmit), and how long it may have been circulating before its detection. As more sequencing data becomes available, a clearer picture of how this virus evolves will emerge. But for now, this work already offers a first glimpse.
At the end of April, a married couple living in Switzerland finished a cruise that had taken them from Ushuaia in Argentina to Saint Helena. On the remote Atlantic island, they said goodbye to their companions of the past few weeks. Most of the passengers were continuing their journey to Cape Verde, but they were returning home. A few days later, they received an email from the cruise operator. It informed them that a rare illness had been detected on board and suggested they self-isolate and monitor their symptoms. The wife displayed no symptoms, but the husband was already experiencing some (hantavirus initially manifests in a way similar to the flu: fever, cough, and gastrointestinal discomfort). He first called his family doctor and then went to the University Hospital of Zurich, where he tested positive for hantavirus.
A team of biologists immediately began working on the genetic samples from this patient. While the world was focused on a cruise ship in the Atlantic, 10 men and women began investigating the cause of all this commotion in two groups, one in Zurich and the other in Geneva. Among them was Francisco Javier Pérez-Rodríguez, originally from Tenerife, Spain, where the MV Hondius had been directed. “On Friday morning, both laboratories obtained the virus sequence, shared it between us to compare it, and then published it together on a blog accessible to everyone,” he explained in a message exchange. The platform is Virological.org.
“We made the diagnosis with a specific PCR test for Andes hantavirus last Tuesday,” explains Pérez-Rodríguez. “The sequencing is also useful because it allows us to conclude that laboratory tests based on the detection of the Andes virus genome (PCR) should be able to detect the virus.”
The virus was sequenced using Illumina technology, which identifies mutations and variants and performs a complete viral sequence. They compared the three segments into which the virus is divided. “And it was observed that there has been no reassortment; that is, no exchange of segments between strains that gives rise to a new virus,” says Pérez-Rodríguez.
With this data, a mutation, which was the experts’ biggest concern, can be ruled out. “The sequence clusters closely with previously described Andean isolates, especially those from Argentina in 2018–2019, which suggests that it is neither a highly divergent variant nor a completely new strain,” explains Estanislao Nistal Villán, a researcher with the virology group at CEU San Pablo University.
The cases Nistal mentions are from an outbreak in Patagonia that surprised the scientific community due to its high transmissibility and which began at a birthday party. There were 34 infections and 11 deaths. Genetic analysis of these cases demonstrated that the Andes strain can be transmitted between humans (the other variants only jump from mice to humans). This was a relative surprise for a virus about which little is known (fewer than 1,000 cases have been recorded and studied) and with very wide variability.
“There is no viral reassortment,” Nistal continues. “There are no signs of segment exchange with other hantaviruses. This points to a stable lineage with what is known.” Viral reassortment is an evolutionary mechanism that occurs when two different variants of the same virus co-infect the same host cell and exchange entire segments of their genetic material (RNA), giving rise to a new virus.
The viral sequencing of the Swiss patient provides some information, but it is limited. Different teams of microbiologists are analyzing the viruses of other patients in this outbreak to reconstruct the chain of infection. Currently, only partial sequencing is available. If their viral genomes are virtually identical, this would support recent human-to-human transmission. Greater genetic diversity among the cases could, however, suggest multiple independent transmission events from mice. We will have to wait to find out.
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