Assessing the genomic sequencing to link SARS-CoV-2

Wastewater surveillance has played a key role in supporting the public health responses to the COVID-19 pandemic, including throughout Victoria, Australia. For much of the pandemic, the Victorian program focused on detecting and tracking SARS-CoV-2 in catchment areas. This information has helped inform the public of infection risk, support decisions on the placement of health resources and guide efforts for early identification of unknown community cases to limit further transmission.

In a pilot study, researchers identified the QIAseq method (a modified commercial version of the ARTIC method used in many WGS-based SARS-CoV-2 surveillance programs worldwide) as a suitable approach. However, they found that it lacked sufficient sensitivity for routine use in Australia, as inferred by its use in Victoria. Highly sensitive methods were developed and optimised to allow the sequencing and analysis of SARS-CoV-2 variants in complex wastewater samples. Researchers show that this approach is robust, highly accurate and provides an important and cost-effective complement to clinical and hospital surveillance programs.

This project has helped to track incursion, spread and predominance of new viral variants with each new successional wave of infections. These efforts forewarn the shifting directions of the pandemic that may preface a new infection wave, supplement efforts to track viral variants in infected patients and support efforts to model the duration and peak of new infection waves as they emerge.