Early Detection of the Emerging SARS-CoV-2 BA.2.86 Lineage Through Wastewater Surveillance Using a Mediator Probe PCR Assay—Shenzhen City,Guangdong Province,China,2023

Introduction:The emergence of the new severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)Omicron sublineage,BA.2.86,has sparked global public health concerns for its potential heightened transmissibility and immune evasion.Utilizing data from Shenzhen’s city-wide wastewater surveillance system,we highlight the presence of the BA.2.86 lineage in Shenzhen.Methods:A mediator probe polymerase chain reaction(PCR)assay was developed to detect the BA.2.86 lineage in wastewater by targeting a specific mutation(Spike:A264D).Between September 19 and December 10,2023,781 wastewater samples from 38 wastewater treatment plants(WWTPs)and 9 pump stations in ten districts of Shenzhen were examined.Through multiple short-amplicon sequencing,three positive samples were identified.Results:The BA.2.86 lineage was identified in the wastewater of Futian and Nanshan districts in Shenzhen on December 2,2023.From December 2 to 10,a total of 21 BA.2.86-positive wastewater samples were found across 6 districts(Futian,Nanshan,Longhua,Baoan,Longgang,and Luohu)in Shenzhen.The weighted average viral load of the BA.2.86 lineage in Shenzhen’s wastewater was 43.5 copies/L on December 2,increased to 219.8 copies/L on December 4,and then decreased to approximately 100 copies/L on December 6,8,and 10.Conclusions:The mediator probe PCR assay,designed for swift detection of low viral concentrations of the BA.2.86 lineage in wastewater samples,shows promise for detecting different SARS-CoV-2 variants.Wastewater surveillance could serve as an early detection system for promptly identifying specific SARS-CoV-2 variants as they emerge.