Speaker
Description
Over the 2023/2024 winter season, we employed a targeted enrichment by hybrid capture method to sequence 1’160 nasopharyngeal swabs from patients across Switzerland presenting with flu-like symptoms. We identified, extracted and produced high-quality genomes of over 25 respiratory virus strains, including strains never before sequenced and publicly shared in Switzerland. Strains ranged from Influenza A/H1N1, SARS-CoV-2, and RSV A and B, to all four seasonal coronaviruses, all four human parainfluenza viruses, metapneumovirus, adenoviruses, rhino- and entero-viruses. We identified 19 co-infections involving more than 15 different virus strains. Among these, RSV A was present in 40% of co-infections.
Utilizing our complete, high-quality genomes in combination with other publicly-available genomes from worldwide sequencing efforts, we built whole-genome phylogenetic trees for each virus strain. We identifed and compared circulating clades between Switzerland and other regions of the world and detected seasonal patterns previously unreported in Switzerland. We also described the circulation patterns of different strain subtypes, such as RSV A and B, and identified differences in Swiss circulating clade patterns.
Additional geographical metadata allowed us to approximate transmission chains within and across different regions of Switzerland. We also characterized introductions into Switzerland, particularly from neighboring countries. Singling out recurring patterns among strains and countries, we were able to identify relevant combinations of strain and country, setting the stage for additional analysis.
With this broad analysis, we characterized the genetic landscape of respiratory viruses in Switzerland. Given that the Swiss sequences distributed across the global trees for all studied strains, and Switzerland’s tightly-connected travel hub, we showed that the Swiss samples spanned global diversity. We are continuing two additional years of collection to confirm and refine our findings.
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