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. 2022 Jun 29;10(3):e0060522.
doi: 10.1128/spectrum.00605-22. Epub 2022 May 3.

Identification of Omicron-Delta Coinfections Using PCR-Based Genotyping

Pavitra Roychoudhury  1   2 , Shishi Luo  3 , Kathleen Hayashibara  4 , Pooneh Hajian  1 , Margaret G Mills  1 , Jean Lozach  5 , Tyler Cassens  3 , Seffir T Wendm  1 , Isabel Arnould  1 , David Becker  3 , Tim Wesselman  5 , Jeremy Davis-Turak  5 , Richard Creager  6 , Eric Lai  7 , Keith R Jerome  1   2 , Tracy Basler  3 , Andrew Dei Rossi  3 , William Lee  3 , Alexander L Greninger  1   2
Affiliations

Identification of Omicron-Delta Coinfections Using PCR-Based Genotyping

Pavitra Roychoudhury et al. Microbiol Spectr. .
No abstract available

Keywords: Delta; Omicron; PCR genotyping; SARS-CoV-2; WGS; coinfection; ddPCR; genomics; variants.

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Conflict of interest statement

The authors declare a conflict of interest. Research reported in this publication was supported by the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health (under award numbers 75N92019P00328, U54EB015408, and U54EB027690) as part of the Rapid Acceleration of Diagnostics (RADxSM) initiative, launched to speed innovation in the development, commercialization, and implementation of technologies for COVID-19 testing. The funders had no role in the decision to submit the work for publication and the views expressed herein are the authors' and do not necessarily represent the views of the National Institutes of Health or the United States Department of Health and Human Services. The authors gratefully acknowledge the originating laboratories responsible for obtaining the specimens, the submitting laboratories where genetic sequence data were generated and shared via the GISAID Initiative, and the GISAID EpiCov Data Curation Team. A.L.G. reports central contract testing for Abbott and research support from Gilead and Merck, unrelated to this work. S.L., T.C., T.B., A.D.R., and W.L. are employees of Helix. K.H. is an employee of Thermo Fisher Scientific. J.L., T.W., J.D.T. are employees of Rosalind Bio.

Figures

FIG 1
FIG 1
Identification of Delta-Omicron coinfection. Allele-specific PCR targeting SARS-CoV-2 allele T13195C of plates containing omicron (T13195C, blue) and delta (T13195, red) infections as well as two co-infection specimens from UW (A) and Helix (B). Mixed samples are clustered in green in the middle of the plot. NTCs are clustered in light blue and are oriented to the origin. (C) RT-ddPCR for coinfection sample 5BG showing amplification of both 452 alleles (L = Omicron; R = Delta) and both 501 alleles (Y* = Omicron, N = Delta) from UW. (D) Allele frequency of signature spike gene mutations commonly of Omicron or Delta or both from deep sequencing of two coinfection samples from UW shows presence of minor alleles corresponding to Omicron and (E) similarly from Helix. Transparency of plotting characters is inversely proportional to depth of coverage at the site in Fig. 1D.
See this image and copyright information in PMC

References

    1. Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, Choga WT, Colquhoun R, Davids M, Deforche K, Doolabh D, Du Plessis L, Engelbrecht S, Everatt J, Giandhari J, Giovanetti M, Hardie D, Hill V, Hsiao N-Y, Iranzadeh A, Ismail A, Joseph C, Joseph R, Koopile L, Kosakovsky Pond SL, Kraemer MUG, Kuate-Lere L, Laguda-Akingba O, Lesetedi-Mafoko O, Lessells RJ, Lockman S, Lucaci AG, Maharaj A, Mahlangu B, Maponga T, Mahlakwane K, Makatini Z, Marais G, Maruapula D, Masupu K, Matshaba M, Mayaphi S, Mbhele N, Mbulawa MB, Mendes A, Mlisana K, Mnguni A, Mohale T, Moir M, Moruisi K, Mosepele M, Motsatsi G, Motswaledi SM, Mphoyakgosi T, Msomi N, Mwangi NP, Naidoo Y, Ntuli N, Nyaga M, Olubayo L, Pillay S, Radibe B, Ramphal Y, Ramphal U, San EJ, Scott L, Shapiro R, Singh L, Lawrence-Smith P, Stevens W, Strydom A, Subramoney K, Tebeila N, Tshiabuila D, Tsui J, Wyk van S, Weaver S, Wibmer KC, Wilkinson E, Wolter N, Zarebski EA, Zuze B, Goedhals D, Preiser W, Treurnicht F, Venter M, Williamson C, Pybus GO, Bhiman J, Glass A, Martin PD, Rambaut A, Gaseitsiwe S, Anne Gottberg von A, Oliveira de T. 2022. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature 603:679–686. doi:10.1038/s41586-022-04411-y. - DOI - PMC - PubMed
    1. Bolze A, White S, Basler T, Rossi AD, Roychoudhury P, Greninger AL, Hayashibara K, Wyman D, Kil E, Dai H, Cassens T, Tsan K, Nguyen J, Ramirez J, Carter S, Cirulli ET, Barrett KS, Belda-Ferre P, Washington NL, Jacobs S, Sandoval E, Becker D, Lu JT, Isaksson M, Lee W, Luo S. 2022. Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination. medRxiv. doi:10.1101/2022.03.09.22272113. - DOI - PMC - PubMed
    1. Mills MG, Hajian P, Bakhash SM, Xie H, Mantzke D, Zhu H, Perchetti GA, Huang M-L, Pepper G, Jerome KR, Roychoudhury P, Greninger AL. 2022. Rapid and accurate identification of SARS-CoV-2 Omicron variants using droplet digital PCR (RT-ddPCR). medRxiv. doi:10.1101/2022.01.11.22268981. - DOI - PMC - PubMed
    1. Perchetti GA, Zhu H, Mills MG, Shrestha L, Wagner C, Bakhash SM, Lin MJ, Xie H, Huang M-L, Mathias P, Bedford T, Jerome KR, Greninger AL, Roychoudhury P. 2021. Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. J Med Virol 93:5931–5941. doi:10.1002/jmv.27155. - DOI - PMC - PubMed
    1. Shrestha L, Lin MJ, Xie H, Mills MG, Bakhash SAM, Gaur VP, Livingston RJ, Castor J, Bruce EA, Botten JW, Huang M-L, Jerome KR, Greninger AL, Roychoudhury P. 2021. Clinical performance characteristics of the Swift Normalase Amplicon Panel for sensitive recovery of SARS-CoV-2 genomes. medRxiv. doi:10.1101/2021.10.22.21265255. - DOI - PMC - PubMed

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