Multiplex PCR amplicon sequencing revealed community transmission of SARS-CoV-2 lineages on the campus of Sichuan University during the outbreak of infection in Chinese Mainland at the end of 2022

During the pandemic of COVID-19, wastewater-based epidemiology has become a powerful epidemic surveillance tool widely used around the world. However, the development and application of this technology in Chinese Mainland are relatively lagging. Herein, we report the first case of community circulation of SARS-CoV-2 lineages monitored by WBE in Chinese Mainland during the infection outbreak at the end of 2022 after the comprehensive relaxation of epidemic prevention policies. During the peak period of infection, six precious sewage samples were collected from the manhole in the student dormitory area of Wangjiang Campus of Sichuan University. According to the results RT-qPCR, the six sewage samples were all positive for SARS-CoV-2 RNA. Based on multiplex PCR amplicon sequencing, the local transmission of SARS-CoV-2 variants at that time was analyzed. The results show that the main virus lineages in sewage have clear evolutionary genetic correlations. Furthermore, the sampling time is very consistent with the timeline of concern for these virus lineages and consistent with the timeline for uploading the nucleic acid sequences of the corresponding lineages in Sichuan to the database. These results demonstrate the reliability of the sequencing results of SARS-CoV-2 nucleic acid in wastewater. Multiplex PCR amplicon sequencing is by far the most powerful analytical tool of WBE, enabling quantitative monitoring of virus lineage prevalence at the community level. HighlightsO_LISix sewage samples were collected on Wangjiang Campus of Sichuan university at the end of 2022. C_LIO_LISARS-CoV-2 nucleic acid was detected in all six sewage samples via qPCR. C_LIO_LIMultiplex PCR amplicon sequencing reveals the local transmission of SARS-CoV-2 lineages. C_LIO_LIMultiplex PCR amplicon sequencing is to date the most powerful WBE tool. C_LI GRAPHICAL ABSTRACT