Although some successes are obvious in our fight against the COVID-19 pandemic, the virus seems to be always ahead of us. Mostly, we are reacting to the problem rather than having some proactive plans. The development of a method utilizing nanobeads to boost the amount of detectable viral RNA in a wastewater sample that successfully detected the Alpha, Delta and Omicron variants up to two weeks before the strains were detected in tests in clinics, could change the paradigm.
Although a huge possibility for early pandemic tracking using wastewater sequencing has long been discussed, two main factors - low-quality sequence data and the inability to estimate relative lineage abundance in mixed samples, were hindering the progress. In an eloquent study published in Nature a few weeks ago, scientists resolved these issues by using nanobeads to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus. They successfully detected emerging variants of concern up to 14 days earlier in wastewater samples. They identified multiple instances of virus spread not captured by clinical genomic surveillance providing a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.