Whole genome sequencing of SARS-CoV-2 to detect novel variants

Whole genome sequencing of SARS-CoV-2 to detect novel variants

This proposal and request for funding is the next step for research into the genomic sequencing of SARS-CoV-2 – a follow on from the world-leading integrated ColoSSoS Project. This proposal aims to provide development of more detailed information in support of health departments and the pandemic response through detection of viral variants.


The imminent opening of borders in Australia could se an increas in the background levels of SARS-CoV-2 in the population. The challenge for public health response will be to locate variants of concern as they enter the country before spreading into the community.

The lack of genetic information encoded by these diagnostic loci is a significant problem when attempting to link wastewater detection to clinical and community sources, or to detect new viral strains of high public health importance, such as the highly transmissible UK N501Y variants. In such applications, the diagnostic markers employed for wastewater surveillance are simply not fit-for-purpose and more genetic information is needed. Whole genome sequencing (WGS) provides the most conclusive and robust approach to addressing these expanded goals.

Primary deliverables:

  1. An evaluation of bulk sampling methods to increase the number of viral genomes captured for wastewater detection and to support genomic sequencing when viral load is at trace levels.
  2. Completion of a controlled, comparative analysis of current leading methods for WGS of wastewater-detected SARS-CoV-2 isolates, assessing the two primary sequencing platforms (Illumina and Oxford Nanopore) used to date, and providing the first analysis, globally, of the benefit of using a hybrid (Illumina plus Oxford Nanopore) sequencing approach to support SNP calling, and viral strain typing and quantitation of SARS-CoV-2 in wastewater.
  3. Assessment of a novel whole genomic amplification methods to target SARS-CoV-2 at trace levels in wastewater samples for WGS applications at comparable sensitivity to RT-qPCR.
  4. Development of gold-standard analytical protocols for detection, identification, tracking and genetic analysis of SARS-CoV-2 variants in wastewater suitable for use with short and/or long-read data.

Secondary deliverables will include:

  1. Independent data to assess the comprehensive capture of viral variants circulating in the community based on clinical genomic sequencing.
  2. Potential insight into viral variants that have longer persistence in faecal shedding through the detection of variants over represented in wastewater detection in the absence of known community transmission events.
  3. Development of a potential front-line tool for detecting introduction of novel, high-risk viral variants into the Australian community.
  4. A testing-ground for strategies to support routine use of WGS methods in wastewater-based epidemiology in future applications.


WaterRA Contact

Dr Kelly Hill

Amount being sought

Seeking $40k contribution per organisation per FY for 2 FYs ($80k total)

Due Date

29th Sep, 2021