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Li J, Cheng R, Bian Z, Niu J, Xia J, Mao G, Liu H, Wu C, Hao C. Development of multiplex allele-specific RT-qPCR assays for differentiation of SARS-CoV-2 Omicron subvariants. Appl Microbiol Biotechnol 2024; 108:35. [PMID: 38183475 DOI: 10.1007/s00253-023-12941-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 01/08/2024]
Abstract
Quick differentiation of current circulating variants and the emerging recombinant variants of SARS-CoV-2 is essential to monitor their transmissions. However, the widely applied gene sequencing method is time-consuming and costly especially when facing recombinant variants, because a large part or whole genome sequencing is required. Allele-specific reverse transcriptase real time RT-PCR (RT-qPCR) represents a quick and cost-effective method for SNP (single nucleotide polymorphism) genotyping and has been successfully applied for SARS-CoV-2 variant screening. In the present study, we developed a panel of 5 multiplex allele-specific RT-qPCR assays targeting 20 key mutations for quick differentiation of the Omicron subvariants (BA.1 to BA.5 and their descendants) and the recombinant variants (XBB.1 and XBB.1.5). Two parallel multiplex RT-qPCR reactions were designed to separately target the prototype allele and the mutated allele of each mutation in the allele-specific RT-qPCR assay. Optimal annealing temperatures, primer and probe dosage, and time for annealing/extension for each reaction were determined by multi-factor and multi-level orthogonal test. The variation of Cp (crossing point) values (ΔCp) between the two multiplex RT-qPCR reactions was applied to determine if a mutation occurs or not. SARS-CoV-2 subvariants and related recombinant variants were differentiated by their unique mutation patterns. The developed multiplex allele-specific RT-qPCR assays exhibited excellent analytical sensitivities (with limits of detection (LoDs) of 1.47-18.52 copies per reaction), wide linear detection ranges (109-100 copies per reaction), good amplification efficiencies (88.25 to 110.68%), excellent reproducibility (coefficient of variations (CVs) < 5% in both intra-assay and inter-assay tests), and good clinical performances (99.5-100% consistencies with Sanger sequencing). The developed multiplex allele-specific RT-qPCR assays in the present study provide an alternative tool for quick differentiation of the SARS-CoV-2 Omicron subvariants and their recombinant variants. KEY POINTS: • A panel of five multiplex allele-specific RT-qPCR assays for quick differentiation of 11 SARS-CoV-2 Omicron subvariants (BA.1, BA.2, BA.4, BA.5, and their descendants) and 2 recombinant variants (XBB.1 and XBB.1.5). • The developed assays exhibited good analytical sensitivities and reproducibility, wide linear detection ranges, and good clinical performances, providing an alternative tool for quick differentiation of the SARS-CoV-2 Omicron subvariants and their recombinant variants.
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Affiliation(s)
- Jianguo Li
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China.
| | - Ruiling Cheng
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Zixin Bian
- College of Life Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Jiahui Niu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Juan Xia
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Guoli Mao
- Shanxi Guoxin Caregeno Biotechnology Co., Ltd., Taiyuan, 030032, People's Republic of China
| | - Hulong Liu
- Shanxi Guoxin Caregeno Biotechnology Co., Ltd., Taiyuan, 030032, People's Republic of China
| | - Changxin Wu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Chunyan Hao
- School of Environment and Resources, Taiyuan University of Science and Technology, Taiyuan, 030024, People's Republic of China.
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Queiroz DC, Carobin NV, de Araújo E Santos LCG, Fonseca PLC, Braga-Paz IL, Dias RC, Ferreira JGG, Freitas TR, Menezes D, Nolasco SCVM, Ribeiro SR, Ribeiro TS, do Amaral Xavier L, Gomes KB, de Paula Sabino A, de Aguiar RS, de Souza RP. SARS-CoV-2 Omicron BA.1, BA.2, and XAG identification during routine surveillance on a university campus in Belo Horizonte, Brazil, 2022. Braz J Microbiol 2022; 53:2009-2014. [PMID: 36272063 PMCID: PMC9589559 DOI: 10.1007/s42770-022-00848-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/12/2022] [Indexed: 11/24/2022] Open
Abstract
We report SARS-CoV-2 genomic surveillance results between Belo Horizonte, Brazil’s third and fourth case waves. Samples were obtained through a routine university monitoring COVID-19 program from the 9th to the 22nd epidemiological weeks (March and June 2022). We identified ten samples from the BA.1 clade (BA.1, BA.1.1, and BA.1.14.1 lineages) and 45 samples from the BA.2 clade (BA.2, BA.2.56, BA.2.9, BA.2.62, BA.2.23, BA.2.81, and BA.2.10). We observed progressive replacement of the BA.1 by the BA.2 clade. Furthermore, two XAG recombinants were found in the 22nd week. Diversification of the omicron variant seems to have contributed to the resurgence of cases in Belo Horizonte, similarly to what has been reported in South Africa.
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Affiliation(s)
- Daniel Costa Queiroz
- Laboratório de Biologia Integrativa Departamento de Genética Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Natália Virtude Carobin
- Laboratório Institucional de Pesquisa Em Biomarcadores Laboratório de Hematologia Clínica Departamento de Análises Clínicas E Toxicológicas Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 ICB - Pampulha, Minas Gerais, 31270901, Belo Horizonte, Brazil
| | - Luiza Campos Guerra de Araújo E Santos
- Laboratório de Biologia Integrativa Departamento de Genética Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paula Luize Camargos Fonseca
- Laboratório de Biologia Integrativa Departamento de Genética Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Isabela Lorraine Braga-Paz
- Laboratório de Biologia Integrativa Departamento de Genética Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rillery Calixto Dias
- Laboratório de Biologia Integrativa Departamento de Genética Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jorge Gomes Goulart Ferreira
- Laboratório de Biologia Integrativa Departamento de Genética Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Túlio Resende Freitas
- Laboratório Institucional de Pesquisa Em Biomarcadores Laboratório de Hematologia Clínica Departamento de Análises Clínicas E Toxicológicas Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 ICB - Pampulha, Minas Gerais, 31270901, Belo Horizonte, Brazil
| | - Diego Menezes
- Laboratório de Biologia Integrativa Departamento de Genética Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sílvia Cristina Verde Mendes Nolasco
- Laboratório Institucional de Pesquisa Em Biomarcadores Laboratório de Hematologia Clínica Departamento de Análises Clínicas E Toxicológicas Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 ICB - Pampulha, Minas Gerais, 31270901, Belo Horizonte, Brazil
| | - Simone Rodrigues Ribeiro
- Laboratório Institucional de Pesquisa Em Biomarcadores Laboratório de Hematologia Clínica Departamento de Análises Clínicas E Toxicológicas Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 ICB - Pampulha, Minas Gerais, 31270901, Belo Horizonte, Brazil
| | - Thaís Salviana Ribeiro
- Laboratório Institucional de Pesquisa Em Biomarcadores Laboratório de Hematologia Clínica Departamento de Análises Clínicas E Toxicológicas Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 ICB - Pampulha, Minas Gerais, 31270901, Belo Horizonte, Brazil
| | - Laura do Amaral Xavier
- Laboratório Institucional de Pesquisa Em Biomarcadores Laboratório de Hematologia Clínica Departamento de Análises Clínicas E Toxicológicas Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 ICB - Pampulha, Minas Gerais, 31270901, Belo Horizonte, Brazil
| | - Karina Braga Gomes
- Laboratório Institucional de Pesquisa Em Biomarcadores Laboratório de Hematologia Clínica Departamento de Análises Clínicas E Toxicológicas Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 ICB - Pampulha, Minas Gerais, 31270901, Belo Horizonte, Brazil
| | - Adriano de Paula Sabino
- Laboratório Institucional de Pesquisa Em Biomarcadores Laboratório de Hematologia Clínica Departamento de Análises Clínicas E Toxicológicas Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 ICB - Pampulha, Minas Gerais, 31270901, Belo Horizonte, Brazil.
| | - Renato Santana de Aguiar
- Laboratório de Biologia Integrativa Departamento de Genética Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil. .,Instituto D'OR de Pesquisa E Ensino, Rio de Janeiro, Brazil.
| | - Renan Pedra de Souza
- Laboratório de Biologia Integrativa Departamento de Genética Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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