Circulation of SARS-CoV-2 Omicron sub-lineages revealed by multiplex genotyping RT-qPCR assays for sewage surveillance.

Sewage surveillance has proven to be an essential complementary tool to clinical diagnosis in combating the COVID-19 pandemic by tracking the spread of the SARS-CoV-2 virus and evaluating infection levels in populations. With the striking spreading and continuous evolution of SARS-CoV-2 Omicron VOC that characterized with higher transmissibility and potential immune evasion, there is an urgent need for the rapid surveillance of this prevalent strain and its sub-lineages in sewage. In this study, based on three multiplex allele-specific (AS) RT-qPCR assays, we established a rapid and high-throughput detection workflow for the simultaneous discrimination of Omicron sub-lineages BA.2.2, BA.2.12.1, BA.4 and BA.5 (hereafter referred to as BA.4/BA.5) to track their community circulation in Hong Kong. All primer-probe sets in the multiplex assays could correctly discriminate and quantitate their target genotypes with high sensitivity and specificity, even when multiple variants co-existed in the sewage samples. Using the established multiplex assays, the trends of SARS-CoV-2 total viral load and variant dynamics in influent samples collected from 11 wastewater treatment plants (WWTPs) during June 2022 and September 2022, aligned with the clinical data, successfully unveiling the swift emergence and predominance of Omicron BA.4/BA.5 in Hong Kong. The study highlights the feasibility and applicability of multiplex RT-qPCR assays for monitoring epidemic trends and tracking variant displacement dynamics in sewage samples, providing a more rapid, high-throughput and cost-effective alternative to enhance the current sewage surveillance system.

Ding J ，Xu X ，Deng Y ，Zheng X ，Zhang T ... -  《-》

Development of multiplex allele-specific RT-qPCR assays for differentiation of SARS-CoV-2 Omicron subvariants.

Li J ，Cheng R ，Bian Z ，Niu J ，Xia J ，Mao G ，Liu H ，Wu C ，Hao C ... -  《-》

Combined Use of RT-qPCR and NGS for Identification and Surveillance of SARS-CoV-2 Variants of Concern in Residual Clinical Laboratory Samples in Miami-Dade County, Florida.

Carattini YL ，Griswold A ，Williams S ，Valiathan R ，Zhou Y ，Shukla B ，Abbo LM ，Parra K ，Jorda M ，Nimer SD ，Sologon C ，Gallegos HR ，Weiss RE ，Ferreira T ，Memon A ，Paige PG ，Thomas E ，Andrews DM ... -  《Viruses-Basel》

Co-incidence of BA.1 and BA.2 at the start of Singapore's Omicron wave revealed by Community and University Campus wastewater surveillance.

Wastewater surveillance (WWS) has been globally recognised to be a useful tool in quantifying SARS-CoV-2 RNA at the community and residential levels without biases associated with case-reporting. The emergence of variants of concern (VOCs) have given rise to an unprecedented number of infections even though populations are increasingly vaccinated. This is because VOCs have been reported to possess higher transmissibility and can evade host immune responses. The B.1.1.529 lineage (Omicron) has severely disrupted global plans to return to normalcy. In this study, we developed an allele-specific (AS) RT-qPCR assay which simultaneously targets the stretch of deletions and mutations in the spike protein from position 24-27 for quantitative detection of Omicron BA.2. Together with previous assays that detect mutations associated with Omicron BA.1 (deletion at position 69 and 70) and all Omicron (mutation at position 493 and 498), we report the validation and time series of these assays from September 2021 to May 2022 using influent samples from two wastewater treatment plants and across four University campus sites in Singapore. Viral RNA concentrations at the treatment plants corroborate with locally reported clinical cases, AS RT-qPCR assays revealed co-incidence of Omicron BA.1 and BA.2 on 12 January 2022, almost two months after initial BA.1 detection in South Africa and Botswana. BA.2 became the dominant variant by the end of January 2022 and completely displaced BA.1 by mid-March 2022. University campus sites were similarly positive for BA.1 and/or BA.2 in the same week as first detection at the treatment plants, where BA.2 became rapidly established as the dominant lineage within three weeks. These results corroborate clinical incidence of the Omicron lineages in Singapore and indicate minimal silent circulation prior to January 2022. The subsequent simultaneous spread of both variant lineages followed strategic relaxation of safe management measures upon meeting nationwide vaccination goals.

Chua FJD ，Kim SY ，Hill E ，Cai JW ，Lee WL ，Gu X ，Afri Affandi SA ，Kwok WCG ，Ng W ，Leifels M ，Armas F ，Chandra F ，Chen H ，Alm EJ ，Tay M ，Wong CCJ ，Ng LC ，Wuertz S ，Thompson JR ... -  《-》

Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance.

Chung HY ，Jian MJ ，Chang CK ，Lin JC ，Yeh KM ，Chen CW ，Hsieh SS ，Hung KS ，Tang SH ，Perng CL ，Chang FY ，Wang CH ，Shang HS ... -  《Microbiology Spectrum》