New emerging viruses require fast reactions and up-to-date monitoring of the spread of their variants in order to react in a timely fashion. Switzerland ran a surveillance program of variants of SARS-CoV-2 in clinical tests until January 2023. Thanks to its flexibility, the SIB Software Resource V-pipe played a key role in this surveillance from very early on, as it performed the analysis of data for the Swiss SARS-CoV-2 sequencing consortium (S3C), that published 75’000 sequences on ENA and GISAID – about half of Switzerland’s total submissions - via with the help of the Swiss Pathogen Surveillance (SPSP). The data have been instrumental in tracking variants (10.1101/2020.10.14.20212621, 10.1016/j.epidem.2021.100480) and in providing crucial information to support the decision-making process of public health authorities (10.1126/scitranslmed.abn7979).
Environmental surveillance of the SARS-CoV-2 pandemic, such as wastewater-based monitoring has become an increasingly important source of information on the spread of variants since clinical tests declined and are currently close to disappearing. The SIB Software Resource V-pipe, including its components specialized in the analysis of wastewater, are at the core of the ongoing wastewater-based SARS-CoV-2 variant monitoring commissioned by the Swiss Federal Office of Public Health, a cornerstone of the current pandemic surveillance in Switzerland. These surveillance efforts enable early warning of the introduction of new variants, provides estimates of their spread, and evaluates epidemiological characteristics, earlier than traditional clinical surveillance and at a fraction of the cost (10.1038/s41564-022-01185-x, 10.1101/2022.11.02.22281825, 10.4414/SMW.2022.w30202)
In late 2021, as the Omicron variant emerged, tracking its spread has been critical for the understanding of the dynamics of the SARS-CoV-2 pandemic. The software component COJAC, developed at SIB as part of the bioinformatics workflow V-pipe, has been used by the UK Health Security Agency to monitor the spread of Omicron variant across 450 sites in the UK (Omicron, VOC- 21NOV-01 (B.1.1.529) Technical briefing 30).
Analysis of wastewater surveillance data requires complex steps to detect the early presence and estimate the relative abundances of viral variants. By integrating COJAC and LolliPop in its workflow, V-pipe drastically simplifies this work. Autumn 2023, V-pipe is being applied in a surveillance program in Northern Italy at Arpa Piemonte to help reduce the tedious work in searching for BA.2.86.
Understanding the interaction between human hosts and animal reservoirs is of crucial importance both for understanding current epidemics and for better anticipating future zoonotic pandemics. The SIB Software Resource V-pipe has been used on samples provided by VetSuisse from viral tests on companion pets living in proximity with COVID-19-infected owners. Results have helped to gain a better understanding of the transmission chains between humans and their pets, and among the animals themselves (10.3390/v15010245).
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