tetano
Editor, Senior Moderator
Biol Methods Protoc
. 2024 Apr 27;9(1):bpae020.
doi: 10.1093/biomethods/bpae020. eCollection 2024. Detection of SARS-CoV-2 B.1.1.529 (Omicron) variant by SYBR Green-based RT-qPCR
Fadi Abdel-Sater[SUP] 1 [/SUP], Rawan Makki[SUP] 1 [/SUP], Alia Khalil[SUP] 1 [/SUP], Nader Hussein[SUP] 1 [/SUP], Nada Borghol[SUP] 1 [/SUP], Ziad Abi Khattar[SUP] 1 [/SUP], Aline Hamade[SUP] 1 [/SUP], Nathalie Khreich[SUP] 1 [/SUP], Mahoumd El Homsi[SUP] 1 [/SUP], Hussein Kanaan[SUP] 1 [/SUP], Line Raad[SUP] 1 [/SUP], Najwa Skafi[SUP] 1 [/SUP], Fatima Al-Nemer[SUP] 1 [/SUP], Zeinab Ghandour[SUP] 1 [/SUP], Nabil El-Zein[SUP] 1 [/SUP], Mhamad Abou-Hamdan[SUP] 1 [/SUP], Haidar Akl[SUP] 1 [/SUP], Eva Hamade[SUP] 1 [/SUP], Bassam Badran[SUP] 1 [/SUP], Kassem Hamze[SUP] 1 [/SUP]
Affiliations
The coronavirus disease 2019 (COVID-19) pandemic is unceasingly spreading across the globe, and recently a highly transmissible Omicron SARS-CoV-2 variant (B.1.1.529) has been discovered in South Africa and Botswana. Rapid identification of this variant is essential for pandemic assessment and containment. However, variant identification is mainly being performed using expensive and time-consuming genomic sequencing. In this study, we propose an alternative RT-qPCR approach for the detection of the Omicron BA.1 variant using a low-cost and rapid SYBR Green method. We have designed specific primers to confirm the deletion mutations in the spike (S Δ143-145) and the nucleocapsid (N Δ31-33) which are characteristics of this variant. For the evaluation, we used 120 clinical samples from patients with PCR-confirmed SARS-CoV-2 infections, and displaying an S-gene target failure (SGTF) when using TaqPath COVID-19 kit (Thermo Fisher Scientific, Waltham, USA) that included the ORF1ab, S, and N gene targets. Our results showed that all the 120 samples harbored S Δ143-145 and N Δ31-33, which was further confirmed by whole-genome sequencing of 10 samples, thereby validating our SYBR Green-based protocol. This protocol can be easily implemented to rapidly confirm the diagnosis of the Omicron BA.1 variant in COVID-19 patients and prevent its spread among populations, especially in countries with high prevalence of SGTF profile.
Keywords: B.1.1.529; SARS-CoV2 RT-PCR; SGTF; variants of concern.
. 2024 Apr 27;9(1):bpae020.
doi: 10.1093/biomethods/bpae020. eCollection 2024. Detection of SARS-CoV-2 B.1.1.529 (Omicron) variant by SYBR Green-based RT-qPCR
Fadi Abdel-Sater[SUP] 1 [/SUP], Rawan Makki[SUP] 1 [/SUP], Alia Khalil[SUP] 1 [/SUP], Nader Hussein[SUP] 1 [/SUP], Nada Borghol[SUP] 1 [/SUP], Ziad Abi Khattar[SUP] 1 [/SUP], Aline Hamade[SUP] 1 [/SUP], Nathalie Khreich[SUP] 1 [/SUP], Mahoumd El Homsi[SUP] 1 [/SUP], Hussein Kanaan[SUP] 1 [/SUP], Line Raad[SUP] 1 [/SUP], Najwa Skafi[SUP] 1 [/SUP], Fatima Al-Nemer[SUP] 1 [/SUP], Zeinab Ghandour[SUP] 1 [/SUP], Nabil El-Zein[SUP] 1 [/SUP], Mhamad Abou-Hamdan[SUP] 1 [/SUP], Haidar Akl[SUP] 1 [/SUP], Eva Hamade[SUP] 1 [/SUP], Bassam Badran[SUP] 1 [/SUP], Kassem Hamze[SUP] 1 [/SUP]
Affiliations
- PMID: 38680163
- PMCID: PMC11055497
- DOI: 10.1093/biomethods/bpae020
The coronavirus disease 2019 (COVID-19) pandemic is unceasingly spreading across the globe, and recently a highly transmissible Omicron SARS-CoV-2 variant (B.1.1.529) has been discovered in South Africa and Botswana. Rapid identification of this variant is essential for pandemic assessment and containment. However, variant identification is mainly being performed using expensive and time-consuming genomic sequencing. In this study, we propose an alternative RT-qPCR approach for the detection of the Omicron BA.1 variant using a low-cost and rapid SYBR Green method. We have designed specific primers to confirm the deletion mutations in the spike (S Δ143-145) and the nucleocapsid (N Δ31-33) which are characteristics of this variant. For the evaluation, we used 120 clinical samples from patients with PCR-confirmed SARS-CoV-2 infections, and displaying an S-gene target failure (SGTF) when using TaqPath COVID-19 kit (Thermo Fisher Scientific, Waltham, USA) that included the ORF1ab, S, and N gene targets. Our results showed that all the 120 samples harbored S Δ143-145 and N Δ31-33, which was further confirmed by whole-genome sequencing of 10 samples, thereby validating our SYBR Green-based protocol. This protocol can be easily implemented to rapidly confirm the diagnosis of the Omicron BA.1 variant in COVID-19 patients and prevent its spread among populations, especially in countries with high prevalence of SGTF profile.
Keywords: B.1.1.529; SARS-CoV2 RT-PCR; SGTF; variants of concern.