tetano
Editor, Senior Moderator
J Clin Microbiol
. 2022 Apr 25;e0017822.
doi: 10.1128/jcm.00178-22. Online ahead of print.
Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification
Priscilla S-W Yeung[SUP] #[/SUP][SUP] 1 [/SUP], Hannah Wang[SUP] #[/SUP][SUP] 1 [/SUP], Mamdouh Sibai[SUP] 1 [/SUP], Daniel Solis[SUP] 1 [/SUP], Fumiko Yamamoto[SUP] 1 [/SUP], Naomi Iwai[SUP] 2 [/SUP], Becky Jiang[SUP] 2 [/SUP], Nathan Hammond[SUP] 3 [/SUP], Bernadette Truong[SUP] 2 [/SUP], Selamawit Bihon[SUP] 2 [/SUP], Suzette Santos[SUP] 2 [/SUP], Marilyn Mar[SUP] 2 [/SUP], Claire Mai[SUP] 3 [/SUP], Kenji O Mfuh[SUP] 2 [/SUP], Jacob A Miller[SUP] 4 [/SUP], ChunHong Huang[SUP] 1 [/SUP], Malaya K Sahoo[SUP] 1 [/SUP], James L Zehnder[SUP] 1 [/SUP], Benjamin A Pinsky[SUP] 1 2 5 [/SUP]
Affiliations
Abstract
The ability to distinguish between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) is of ongoing interest due to differences in transmissibility, responses to vaccination, clinical prognosis, and therapy. Although detailed genetic characterization requires whole-genome sequencing (WGS), targeted nucleic acid amplification tests can serve a complementary role in clinical settings, as they are more rapid and accessible than sequencing in most laboratories. We designed and analytically validated a two-reaction multiplex reverse transcription-quantitative PCR (RT-qPCR) assay targeting spike protein mutations L452R, E484K, and N501Y in reaction 1 and del69-70, K417N, and T478K in reaction 2. This assay had 95 to 100% agreement with WGS for 502 upper respiratory tract swab samples collected between 26 April 2021 and 1 August 2021, consisting of 43 Alpha, 2 Beta, 20 Gamma, 378 Delta, and 59 non-VOC infections. Validation in a separate group of 230 WGS-confirmed Omicron variant samples collected in December 2021 and January 2022 demonstrated 100% agreement. This RT-qPCR-based approach can be implemented in clinical laboratories already performing SARS-CoV-2 nucleic acid amplification tests to assist in local epidemiological surveillance and clinical decision-making.
Keywords: COVID-19; Omicron; SARS-CoV-2; variant.
. 2022 Apr 25;e0017822.
doi: 10.1128/jcm.00178-22. Online ahead of print.
Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification
Priscilla S-W Yeung[SUP] #[/SUP][SUP] 1 [/SUP], Hannah Wang[SUP] #[/SUP][SUP] 1 [/SUP], Mamdouh Sibai[SUP] 1 [/SUP], Daniel Solis[SUP] 1 [/SUP], Fumiko Yamamoto[SUP] 1 [/SUP], Naomi Iwai[SUP] 2 [/SUP], Becky Jiang[SUP] 2 [/SUP], Nathan Hammond[SUP] 3 [/SUP], Bernadette Truong[SUP] 2 [/SUP], Selamawit Bihon[SUP] 2 [/SUP], Suzette Santos[SUP] 2 [/SUP], Marilyn Mar[SUP] 2 [/SUP], Claire Mai[SUP] 3 [/SUP], Kenji O Mfuh[SUP] 2 [/SUP], Jacob A Miller[SUP] 4 [/SUP], ChunHong Huang[SUP] 1 [/SUP], Malaya K Sahoo[SUP] 1 [/SUP], James L Zehnder[SUP] 1 [/SUP], Benjamin A Pinsky[SUP] 1 2 5 [/SUP]
Affiliations
- PMID: 35465708
- DOI: 10.1128/jcm.00178-22
Abstract
The ability to distinguish between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) is of ongoing interest due to differences in transmissibility, responses to vaccination, clinical prognosis, and therapy. Although detailed genetic characterization requires whole-genome sequencing (WGS), targeted nucleic acid amplification tests can serve a complementary role in clinical settings, as they are more rapid and accessible than sequencing in most laboratories. We designed and analytically validated a two-reaction multiplex reverse transcription-quantitative PCR (RT-qPCR) assay targeting spike protein mutations L452R, E484K, and N501Y in reaction 1 and del69-70, K417N, and T478K in reaction 2. This assay had 95 to 100% agreement with WGS for 502 upper respiratory tract swab samples collected between 26 April 2021 and 1 August 2021, consisting of 43 Alpha, 2 Beta, 20 Gamma, 378 Delta, and 59 non-VOC infections. Validation in a separate group of 230 WGS-confirmed Omicron variant samples collected in December 2021 and January 2022 demonstrated 100% agreement. This RT-qPCR-based approach can be implemented in clinical laboratories already performing SARS-CoV-2 nucleic acid amplification tests to assist in local epidemiological surveillance and clinical decision-making.
Keywords: COVID-19; Omicron; SARS-CoV-2; variant.