NEW YORK – An international team has tapped into Austria's epidemiological system and generated new genome sequence data as part of a study aimed at understanding transmission events and viral mutation patterns during superspreading events in that country's initial wave of SARS-CoV-2 infections this spring.
For a paper published in Science Translational Medicine on Monday, researchers from Austria, the US, and Spain performed deep whole-genome sequencing on SARS-CoV-2 isolates from hundreds of individuals diagnosed with COVID-19 between late February and early May. They then combined that data with more than 7,700 other SARS-CoV-2 sequences from Europe, as well as with available epidemiological data, for a phylogenetic epidemiology analysis.
"Our results provide fully integrated genetic and epidemiological evidence for continental spread of SARS-CoV-2 from Austria and establish fundamental transmission properties in the human population," corresponding author Andreas Bergthaler, a researcher at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, and his colleagues wrote.
The data highlighted superspreader events related to winter tourism destinations, the team reported, including a cluster of genetically similar viruses that infected individuals who visited the Ischgl ski resort in the Tyrolean Alps, as well as some individuals living in the region. SARS-CoV-2 isolates in that cluster shared a mutation profile that placed them into a clade known as 20C, which was also found in parts of France in late February and subsequently spread to Iceland, other parts of Europe, and beyond.
"Together, these observations and epidemiological evidence support the notion that the SARS-CoV-2 outbreak in Austria propagated to Iceland," the authors explained, adding that "[o]ne week after the occurrence of SARS-CoV-2 strains with this mutation profile in France and Ischgl, an increasing number of related strains based on the same mutation profile could be found across continents, for example in New York City."
The researchers also saw signs of another superspreader event in Vienna, where an individual infected by a family member who visited northern Italy is thought to have transmitted the virus to several others while participating in a sports activity indoors. At least one of those individuals, in turn, continued to pass on the virus — transmission patterns supported by the mutation profiles in the individual viruses.
"The transmission chain started with a returnee from Italy," co-first authors Alexandra Popa and Jakob-Wendelin Genger, both researchers at the CeMM Research Center, said in a statement. "Within 24 days, the SARS-CoV-2 virus spread in the greater Vienna region via public and social events in closed rooms."
Consequently, the study's authors suggested that both the Vienna cluster and the outbreak at the ski resort "originated from crowded indoor events (an Apre Ski bar and a sports class, respectively), which are now appreciated as high-risk situations for superspreading events."
Based on variant frequency patterns and related bottleneck analyses, the team estimated that around 1,000 infectious viral particles on average were passed from one individual to the next becoming infected. And with samples collected over time from 31 individuals with COVID-19, meanwhile, the investigators were able to follow new mutations in the SARS-CoV-2 isolates as the viruses evolved within each infected person, including five people with fatal infections.
"We observed diverse mutation patterns across individual patients and over time," the authors noted, explaining that "patient-specific dynamics of viral mutation frequencies may reflect the effect of host-intrinsic factors such as immune responses or the patients' overall health, and extrinsic factors such as different treatment protocols."