tetano
Editor, Senior Moderator
Microbiol Spectr
. 2022 Sep 15;e0322222.
doi: 10.1128/spectrum.03222-22. Online ahead of print.
Accessible and Adaptable Multiplexed Real-Time PCR Approaches to Identify SARS-CoV-2 Variants of Concern
Ting Yan[SUP] #[/SUP][SUP] 1 [/SUP], Ye Xu[SUP] #[/SUP][SUP] 1 [/SUP], Rongrong Zheng[SUP] #[/SUP][SUP] 2 [/SUP], Xiaohong Zeng[SUP] 2 [/SUP], Zehui Chen[SUP] 2 [/SUP], Su Lin[SUP] 1 [/SUP], Zihan Xia[SUP] 1 [/SUP], Yiqun Liao[SUP] 1 [/SUP], Yongyou Zhang[SUP] 1 [/SUP], Qingge Li[SUP] 1 [/SUP]
Affiliations
Abstract
Rapid identification and continuous surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are critical for guiding the response to the COVID-19 pandemic. Whole-genome sequencing (WGS) is a preferred tool for this aim, but many laboratories suffer from a lack of resources to support population-level sequencing. Here, we describe two PCR strategies targeting spike protein mutations to identify the Alpha, Delta, and Omicron variants. Signature mutations were selected using a dedicated bioinformatic program. The selected mutations in Alpha and Delta variants were detected using multicolor melting curve analysis (MMCA). Thirty-two mutations of the Omicron variant were targeted using the MeltArray approach in one reaction, which was able to detect the Omicron subvariants BA.1, BA.2, BA.3, and BA.4/5. The limits of detection varied from five to 50 copies of RNA templates/reactions. No cross-reactivity was observed with nine other respiratory viruses, including other coronaviruses. We validated the MMCA and MeltArray assays using 309 SARS-CoV-2 positive samples collected at different time points. These assays exhibited 98.3% to 100% sensitivity and 100% specificity compared with WGS. Multiplexed real-time PCR strategies represent an alternative tool capable of identifying current SARS-CoV-2 VOCs, adaptable for emerging variants and accessible for laboratories using existing equipment and personnel. IMPORTANCE Rapid detection and mutation surveillance of SARS-CoV-2 VOCs is crucial for COVID-19 control, management, and prevention. We developed two rapid molecular assays based on the real-time PCR platform to identify important variants of concern, including the Omicron variant with a large number of mutations. Signature mutations were selected by an R program. Then, MMCA assays were established for Alpha and Delta variants, and a MeltArray assay targeting 32 mutations was developed for Omicron variant. These multiplexed PCR assays could be performed in a 96-well real-time PCR instrument within 2.5 h, offering a high-throughput choice for dynamic monitoring of SARS-CoV-2 VOCs in a standard microbiology laboratory.
Keywords: Omicron variant; SARS-CoV-2 VOCs; multiplex PCR; rapid genotyping.
. 2022 Sep 15;e0322222.
doi: 10.1128/spectrum.03222-22. Online ahead of print.
Accessible and Adaptable Multiplexed Real-Time PCR Approaches to Identify SARS-CoV-2 Variants of Concern
Ting Yan[SUP] #[/SUP][SUP] 1 [/SUP], Ye Xu[SUP] #[/SUP][SUP] 1 [/SUP], Rongrong Zheng[SUP] #[/SUP][SUP] 2 [/SUP], Xiaohong Zeng[SUP] 2 [/SUP], Zehui Chen[SUP] 2 [/SUP], Su Lin[SUP] 1 [/SUP], Zihan Xia[SUP] 1 [/SUP], Yiqun Liao[SUP] 1 [/SUP], Yongyou Zhang[SUP] 1 [/SUP], Qingge Li[SUP] 1 [/SUP]
Affiliations
- PMID: 36106882
- DOI: 10.1128/spectrum.03222-22
Abstract
Rapid identification and continuous surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are critical for guiding the response to the COVID-19 pandemic. Whole-genome sequencing (WGS) is a preferred tool for this aim, but many laboratories suffer from a lack of resources to support population-level sequencing. Here, we describe two PCR strategies targeting spike protein mutations to identify the Alpha, Delta, and Omicron variants. Signature mutations were selected using a dedicated bioinformatic program. The selected mutations in Alpha and Delta variants were detected using multicolor melting curve analysis (MMCA). Thirty-two mutations of the Omicron variant were targeted using the MeltArray approach in one reaction, which was able to detect the Omicron subvariants BA.1, BA.2, BA.3, and BA.4/5. The limits of detection varied from five to 50 copies of RNA templates/reactions. No cross-reactivity was observed with nine other respiratory viruses, including other coronaviruses. We validated the MMCA and MeltArray assays using 309 SARS-CoV-2 positive samples collected at different time points. These assays exhibited 98.3% to 100% sensitivity and 100% specificity compared with WGS. Multiplexed real-time PCR strategies represent an alternative tool capable of identifying current SARS-CoV-2 VOCs, adaptable for emerging variants and accessible for laboratories using existing equipment and personnel. IMPORTANCE Rapid detection and mutation surveillance of SARS-CoV-2 VOCs is crucial for COVID-19 control, management, and prevention. We developed two rapid molecular assays based on the real-time PCR platform to identify important variants of concern, including the Omicron variant with a large number of mutations. Signature mutations were selected by an R program. Then, MMCA assays were established for Alpha and Delta variants, and a MeltArray assay targeting 32 mutations was developed for Omicron variant. These multiplexed PCR assays could be performed in a 96-well real-time PCR instrument within 2.5 h, offering a high-throughput choice for dynamic monitoring of SARS-CoV-2 VOCs in a standard microbiology laboratory.
Keywords: Omicron variant; SARS-CoV-2 VOCs; multiplex PCR; rapid genotyping.