Detection of SARS-CoV-2 Variants of Concern with Tiling Amplicon Sequencing from Wastewater

The emerging variants of concern (VOCs) of SARS-CoV-2, e.g., Alpha, Beta, Gamma, Delta, and Omicron, have constrained the global response to the COVID-19 pandemic. They challenge our current capability to identify and distinguish variants from wastewater, due to the high likelihood of viral RNA degradation and the prior knowledge required for primer design. This study focused on the detection of multiple VOCs of SARS-CoV-2 using a high-throughput, multiplexed, amplicon-based sequencing technology, namely, ATOPlex. We first demonstrated that this method can discern multiple variants from artificial samples consisting of four synthetic strains of SARS-CoV-2. The ability of ATOPlex to identify VOCs was further validated using real wastewater samples collected from both an international passenger flight and local wastewater treatment plants. On the basis of phylogenetic analysis and the identification of single-nucleotide polymorphism on the genomes, the ATOPlex method was shown to be effective in detecting three VOCs, including two Beta variants and one Delta variant from either local wastewater or flight sewage samples, which were phylogenetically close to the variants that originated from France, Philippines, and the United States. We found this method is mutation-independent, rendering it a tool for proactive detection of SARS-CoV-2 VOCs in wastewater for the application of wastewater-based epidemiology.

CoLabS: A collaborative space for transdisciplinary work in sustainable community development.

Currently, the need for transdisciplinary approaches and collaboration, to reduce the gap between science and practice, is continuously rising along with the need for sustainable development. An increase in knowledge transfer, meetings and overall communication among researchers and practitioners is a logical consequence of the previous. However, the resulting higher transaction costs, mainly related to transportation-related greenhouse gas emissions (and additional financial costs) involved in face-to-face meetings, are in direct conflict with the urgent need to reduce our carbon footprint. This research explored the development of an online platform, "CoLabS", specifically designed as a virtual meeting and learning space to support collaboration within and between communities to accelerate sustainable community development efforts. While the move towards online collaboration in virtual environments has steadily increased in the past decade, it has now become essential due to the COVID-19 pandemic. Based on the feedback provided by focus groups, the collaboratory platform's design and usability as well as the technical aspects and its functionality are discussed in this paper.