Characterizing co-circulating respiratory virus genomic diversity in Switzerland with hybrid-capture sequencing and phylogenetic reconstructions: Insights into the 2023/24 season

Respiratory viruses circulate yearly with strain-specific patterns. Although SARS-CoV-2 and Influenza A/B genomic surveillance is well-developed, most respiratory viruses are unevenly monitored, lacking geographical diversity to capture wider population dynamics. Consequently, insights into respiratory virus evolution are limited. We investigated the genetic diversity of these viruses within one country. During the 2023/24 season, we conducted whole-genome sequencing of 1'129 clinical samples using a hybrid-capture protocol. These samples were pre-tested by real-time PCR panels throughout Switzerland. Leveraging publicly-available full-length genomes, we constructed background datasets representative of geographical diversity and built 16 phylogenies covering the diversity of high-quality viral genomes produced from this study. We detected viral genomes in 632 samples, including 55.6% multi-positive infections (n = 352/632), and recovered high-quality genomes in 73% (n = 461/632) of cases, including 3.9% of co-infections (n = 18/461), from 454 PCR-positive and 7 PCR-negative samples. For 56% of samples (n = 634/1129), the hybrid-capture detection result was concordant with the PCR-result (at least one strain detected by PCR was also detected by sequencing, in addition to other viruses). The four most prevalent viruses were Influenza A/H1N1, SARS-CoV-2, RSV-A, and HPIV-3, and their seasonal spread was consistent with national wastewater monitoring and influenza-like illness reports. Swiss viral genomes were representative of the global genomic diversity, with evidence for multiple introductions into Switzerland, and we identified putative Swiss clusters. In this proof-of-concept study, we focus on 3 viruses (Influenza A/H1N1, RSV-A/B, and HPIV-3), and we demonstrate the streamlined implementation of a broad respiratory virus genomic surveillance workflow with an off-the-shelf protocol and publicly-available software. In addition, we highlight additional evolutionary insights that can only be derived from genomic surveillance. Going forward, this dataset will be a useful resource for future investigations into respiratory viral genomic diversity.