Abstract
We developed a new test system to detect the omicron variant of SARS-CoV-2 using allele-specific reverse transcription PCR and estimated the frequency of its detection in patients living in the Novosibirsk Region. Clinical samples were divided into 3 groups: samples collected from December 1 to December 30, 2021 (group 1; n=66), from December 30, 2021 to January 10, 2022 (group 2; n=20), and from January 11 to January 22, 2022 (group 3; n=101). Based on the identification of 5 mutations specific to SARS-CoV-2 (B.1.1.529), two systems of oligonucleotide primers and probes were developed for detecting this coronavirus genotype in clinical samples. Limit of detection (LOD95) was 4×103 genome equivalents per 1 ml of clinical sample for the first test system and 2×103 for the for the second test system. The omicron variant of SARS-CoV-2 was absent in group 1 of studied samples, but was detected in 20% (4/20) of group 2 samples and 88% of group 2 samples collected within less than 2 weeks of January 2022. Using developed test system, we showed that in less than 2 weeks the omicron variant has become dominant in patients, which confirms previously published data on its exceptional contagiousness.
Key Words: SARS-CoV 2, coronavirus, mutations, omicron variant, allele-specific reverse transcription PCR (AS-RT-PCR)
Footnotes
Translated from Byulleten’ Eksperimental’noi Biologii i Meditsiny, Vol. 173, No. 2, pp. 205-211, February, 2022
References
- 1.Callaway E. Heavily mutated Omicron variant puts scientists on alert. Nature. 2021;600:21. doi: 10.1038/d41586-021-03552-w. [DOI] [PubMed] [Google Scholar]
- 2.Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, Pearson CAB, Russell TW, Tully DC, Washburne AD, Wenseleers T, Gimma A, Waites W, Wong KLM, van Zandvoort K, Silverman JD; CMMID COVID-19 Working Group; COVID-19 Genomics UK (COG-UK) Consortium, Diaz-Ordaz K, Keogh R, Eggo RM, Funk S, Jit M, Atkins KE, Edmunds WJ. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science. 2021;372(6538):eabg3055. doi: 10.1126/science.abg3055 [DOI] [PMC free article] [PubMed]
- 3.Fisman DN, Tuite AR. Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario. Canada. CMAJ. 2021;193(42):E1619–E1625. doi: 10.1503/cmaj.211248. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Frampton D, Rampling T, Cross A, Bailey H, Heaney J, Byott M, Scott R, Sconza R, Price J, Margaritis M, Bergstrom M, Spyer MJ, Miralhes PB, Grant P, Kirk S, Valerio C, Mangera Z, Prabhahar T, Moreno-Cuesta J, Arulkumaran N, Singer M, Shin GY, Sanchez E, Paraskevopoulou SM, Pillay D, McKendry RA, Mirfenderesky M, Houlihan CF, Nastouli E. Genomic characteristics and clinical effect of the emergent SARS-CoV-2 B.1.1.7 lineage in London, UK: a whole-genome sequencing and hospital-based cohort study. Lancet Infect. Dis. 2021;21(9):1246–1256. doi: 10.1016/S1473-3099(21)00170-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Houhamdi L, Gautret P, Hoang VT, Fournier PE, Colson P, Raoult D. Characteristics of the first 1119 SARS-CoV-2 Omicron variant cases, in Marseille, France, November-December 2021. J. Med. Virol. 2022;94(5):2290–2295. doi: 10.1002/jmv.27613. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Ito K, Piantham C, Nishiura H. Relative instantaneous reproduction number of Omicron SARS-CoV-2 variant with respect to the Delta variant in Denmark. J. Med. Virol. 2022;94(5):2265–2268. doi: 10.1002/jmv.27560. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Kozlov M. How does Omicron spread so fast? A high viral load isn’t the answer. Nature. 2022. doi: 10.1038/d41586-022-00129-z [DOI] [PubMed]
- 8.Lazarevic I, Pravica V, Miljanovic D, Cupic M. Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? Viruses. 2021;13(7):1192. doi: 10.3390/v13071192. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Liu Q, Qin C, Liu M, Liu J. Effectiveness and safety of SARS-CoV-2 vaccine in real-world studies: a systematic review and meta-analysis. Infect. Dis. Poverty. 2021;10(1):132. doi: 10.1186/s40249-021-00915-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Liu Y, Rocklöv J. The reproductive number of the Delta variant of SARS-CoV-2 is far higher compared to the ancestral SARS-CoV-2 virus. J. Travel Med. 2021;28(7):taab124. doi: 10.1093/jtm/taab124 [DOI] [PMC free article] [PubMed]
- 11.Nishiura H, Ito K, Anzai A, Kobayashi T, Piantham C, Rodríguez-Morales AJ. Relative Reproduction Number of SARS-CoV-2 Omicron (B.1.1.529) Compared with Delta Variant in South Africa. J. Clin. Med. 2021;11(1):30. doi: 10.3390/jcm11010030 [DOI] [PMC free article] [PubMed]
- 12.Pouwels KB, Pritchard E, Matthews PC, Stoesser N, Eyre DW, Vihta KD, House T, Hay J, Bell JI, Newton JN, Farrar J, Crook D, Cook D, Rourke E, Studley R, Peto TEA, Diamond I, Walker AS. Effect of Delta variant on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK. Nat. Med. 2021;27(12):2127–2135. doi: 10.1038/s41591-021-01548-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat. Microbiol. 2020;5(11):1403–1407. doi: 10.1038/s41564-020-0770-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Wolter N, Jassat W, Walaza S, Welch R, Moultrie H, Groome M, Amoako DG, Everatt J, Bhiman JN, Scheepers C, Tebeila N, Chiwandire N, du Plessis M, Govender N, Ismail A, Glass A, Mlisana K, Stevens W, Treurnicht FK, Makatini Z, Hsiao NY, Parboosing R, Wadula J, Hussey H, Davies MA, Boulle A, von Gottberg A, Cohen C. Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study. Lancet. 2022;399:437–446. doi: 10.1016/S0140-6736(22)00017-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Wu M, Wall EC, Carr EJ, Harvey R, Townsley H, Mears HV, Adams L, Kjaer S, Kelly G, Warchal S, Sawyer C, Kavanagh C, Queval CJ, Ngai Y, Hatipoglu E, Ambrose K, Hindmarsh S, Beale R, Gamblin S, Howell M, Kassiotis G, Libri V, Williams B, Gandhi S, Swanton C, Bauer DL. Three-dose vaccination elicits neutralising antibodies against omicron. Lancet. 2022;399:715–717. doi: 10.1016/S0140-6736(22)00092-7. [DOI] [PMC free article] [PubMed] [Google Scholar]