Highly sensitive wastewater surveillance of SARS-CoV-2 variants by targeted next-generation amplicon sequencing provides early warning of incursion in Victoria, Australia

Merrett, JE; Nolan, M; Hartman, L; John, N; Flynn, B; Baker, L; Schang, C; McCarthy, D; Lister, D; Cheng, NN; Crosbie, N; Poon, R; Jex, A

Author(s): Merrett, JE; Nolan, M; Hartman, L; John, N; Flynn, B; Baker, L; Schang, C; McCarthy, D; Lister, D; Cheng, NN; Crosbie, N; Poon, R; Jex, A;
Details: Publication Year 2024-07-16,Volume 90,Issue #8,Page e0149723
Journal Title: Applied and Environmental Microbiology
Abstract: The future of the COVID pandemic and its public health and societal impact will be determined by the profile and spread of emerging variants and the timely identification and response to them. Wastewater surveillance of SARS-CoV-2 has been widely adopted in many countries across the globe and has played an important role in tracking infection levels and providing useful epidemiological information that cannot be adequately captured by clinical testing alone. However, novel variants can emerge rapidly, spread globally, and markedly alter the trajectory of the pandemic, as exemplified by the Delta and Omicron variants. Most mutations linked to the emergence of new SARS-CoV-2 variants are found within variable regions of the SARS-CoV-2 Spike protein. We have developed a duplex hemi-nested PCR method that, coupled with short amplicon sequencing, allows simultaneous typing of two of the most highly variable and informative regions of the Spike gene: the N-terminal domain and the receptor binding motif. Using this method in an operationalized public health program, we identified the first known incursion of Omicron BA.1 into Victoria, Australia and demonstrated how sensitive amplicon sequencing methods can be combined with wastewater surveillance as a relatively low-cost solution for early warning of variant incursion and spread.IMPORTANCEThis study offers a rapid, cost-effective, and sensitive approach for monitoring SARS-CoV-2 variants in wastewater. The method's flexibility permits timely modifications, enabling the integration of emerging variants and adaptations to evolving SARS-CoV-2 genetics. Of particular significance for low- and middle-income regions with limited surveillance capabilities, this technique can potentially be utilized to study a range of pathogens or viruses that possess diverse genetic sequences, similar to influenza.
Publisher: ASM
Keywords: Covid-19; Delta; Omicron; SARS-CoV-2; amplicon sequencing; coronavirus; genomic surveillance; wastewater surveillance; wastewater-based epidemiology
Research Division(s): Population Health And Immunity
PubMed ID: 39012098
Publisher's Version: https://doi.org/10.1128/aem.01497-23
Open Access at Publisher's Site: https://doi.org/10.1128/aem.01497-23
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2024-07-26 09:22:58

Last Modified: 2024-08-23 03:11:46