In silico analysis for SARS-CoV-2 detection in the context of genetic variability of the Algerian omicron variant

Document Type : Original article

Authors

1 Biology Department, Faculty of Natural and Life Sciences, University of Mostaganem, Algeria

2 Laboratory of Molecular and Cellular Genetics (LGMC), University of Sciences and Technology of Oran, Algeria

3 High School of Biological Sciences, Oran, Algeria

Abstract

The risk to public health conferred by the Omicron variant is still not completely clear, although its numerous gene mutations have raised concerns regarding its potential for increased transmissibility and immune escape. In this study, we test the compatibility of the different primers and probes available in different commercial kits sold internationally with all the sequences of SARS-CoV-2 analyzed in Algeria until March 2023. The Algerian SARS-CoV-2 Omicron variant sequences were aligned with the Muscle tool using Genious software. We also used primers and probes sequences of seven international RT-qPCR kits; CDC China, Charite Germany, HKU Hong Kong, NIH Thailand, NIID Japan, CDC US, and Pasteur Institute. We used the primer check v2.0 developed by VIROSCIENCE LAB, To identify the different mutations located at the level of primers and probes about the Algerian sequences of SARS-CoV2. Statistical tests were carried out by calculating the c2 test. We found regarding the Forward primer sequences that the two Thailand and Japan kits are less specific to the Algerian version of the SARS-CoV-2 Omicron variant genome compared to the other kits (p=10-6). Furthermore, regarding the Reverse primers and fluorescent Probes, the three kits; Thailand, Japan, and CDC US; are less effective (p=10-6). Regarding all primers and probes, this work allowed us to conclude that the four RT-qPCR kits: CDC China, Charite Germany, NHD Hong Kong, and Pasteur Institute seem to be more specific for the Algerian omicron genome detection and therefore for diagnosis of COVID-19 in Algeria.

Keywords

References

  1. de Groot RJ, Baker SC, Baric RS, Brown CS, Drosten C, Enjuanes L, Fouchier RAM, Galiano M, Gorbalenya AE, Memish ZA, Perlman S, Poon LM, Snijder EJ, Stephens GM, Woo PCY, Zaki AM, Zambon M, Ziebuhr J. Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the Coronavirus study group. J Virol 2013;87:7790-7792.
  2. Corman VM, Muth D, Niemeyer D, Drosten C. Hosts and sources of endemic human coronaviruses. Adv Virus Res 2018;100:163-188.
  3. Tan W, Zhao X, Ma X, Wang W, Niu P, Xu W, Gao GF, Wu G. A novel coronavirus genome identified in a cluster of pneumonia cases-wuhan, China 2019-2020. China CDC Wkly 2020;2:61-62.
  4. Moore SA, Faulkner G, Rhodes RE, Brussoni M, Chulak-Bozzer T, Ferguson LJ, Mitra R, O'Reilly N, Spence JC, Vanderloo LM, Tremblay MS. Impact of the COVID-19 virus outbreak on movement and play behaviours of Canadian children and youth: a national survey. Int J Behav Nutr Phys Act 2020;17:85.
  5. Lounis M. A descriptive study of the current situation of COVID-19 in Algeria. Electron J Gen Med 2020;17:em253
  6. Wang MY, Zhao R, Gao LJ, Gao XF, Wang DP, Cao JM. SARS-CoV-2: Structure, biology, and structure-based therapeutics development. Front Cell Infect Microbiol 2020;10:587269.
  7. Shereen MA, Khan S, Kazmi A, Bashir N, Siddique R. COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses. J Adv Res 2020;24:91-98.
  8. Anantharajah A, Helaers R, Defour JP, Olive N, Kabera F, Croonen L, Deldime F, Vaerman JL, Barbee C, Bodeus M, Scohy A, Verroken A, Rodriquez-Villalobos H, Kabamba-Mukadi B. How to choose the right real-time RT-PCR primer sets for the SARS-CoV-2 genome detection?. J Virol Methods 2021;295:114197.
  9. Alvarez-Diaz DA, Franco-Munoz C, Laiton-Donato K, Usme-Ciro JA, Franco-Sierra ND, Florez-Sanchez AC, Gomez-Rangel S, Rodriguez-Calderon LD, Barbosa-Ramirez J, Ospitia-Baez E, Walteros DM, Ospina-Martinez ML, Mercado-Reyes M. Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia. Infect Genet Evol 2020;84:104390.
  10. Takemae N, Doan YH, Momose F, Saito T, Kageyama T. Development of new SNP genotyping assays to discriminate the omicron variant of SARS-CoV-2. Jpn J Infect Dis 2022;75:411-414.
  11. Brown AN, Lang Y, Zhou J, Franco EJ, Hanrahan KC, Bulitta JB, Drusano GL. Why molnupiravir fails in hospitalized patients. mBio 2022;13:e0291622.
  12. Cosar B, Karagulleoglu ZY, Unal S, Ince AT, Uncuoglu DB, Tuncer G, Kilinc BR, Ozkan YE, Ozkoc HC, Demir IN, Eker A, Karagoz F, Simsek SY, Yasar B, Pala M, Demir A, Atak IN, Mendi AH, Bengi VU, Seval GC, Altuntas EG, Kilic P, Demir-Dora D. SARS-CoV-2 mutations and their viral variants. Cytokine Growth Factor Rev 2022;63:10-22.
  13. Li X, Wang W, Zhao X, Zai J, Zhao Q, Li Y, Chaillon A. Transmission dynamics and evolutionary history of 2019-nCoV. J Med Virol 2020;92:501-511.
  14. Gonzalez-Reiche AS, Alshammary H, Schaefer S, Patel G, Polanco J, Carreno JM, Amoako AA, Rooker A, Cognigni C, Floda D, van de Guchte A, Khalil Z, Farrugia K, Assad N, Zhang J, Alburqueque B, PARIS/PSP study group, Sominsky LA, Gleason C, Srivastava K, Sebra R, Ramirez JD, Banu R, Shrestha P, Krammer F, Pani-Mondolfi A, Sordillo EM, Simon V, van Bakel H. Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants. Nat Commun 2023;14:3235.
  15. Chen J, Wang R, Wang M, Wei GW. Mutations strengthened SARS-CoV-2 infectivity. J Mol Biol 2020;432:5212-5226.
  16. Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID's innovative contribut-ion to global health. Glob Chall 2017;1:33-46.
  17. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792-1797.
  18. Wang R, Hozumi Y, Yin C, Wei GW. Decoding SARS-CoV-2 transmission and evolution and ramifications for COVID-19 diagnosis, vaccine, and medicine. J Chem Inf Model 2020; 60:5853-5865.
  19. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes E, Zhang YZ. A new coronavirus associated with human respiratory disease in China. Nature 2020;579:265-269.
  20. Ferron F, Subissi L, Silveira De Morais AT, Le NTT, Sevajol M, Gluais L, Decroly E, Vonrhein C, Bricogne G, Canard B, Imbert I. Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA. Proc Natl Acad Sci USA 2018; 115:E162-E171.
  21. Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Giorgi EE, Bhattacharya T, Parker MD, Partridge DG, Evans CM, de Silva Tl, LaBranche CC, Montefiori DC. Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2. bioRxiv 2020:2020.04.29.069054.
  22. Bustin SA. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 2000;25:169-193.
  23. de Noronha CM, Mullins JI. Amplimers with 3'-terminal phosphorothioate linkages resist degradation by vent polymerase and reduce Taq polymerase mispriming. PCR Methods Appl 1992;2:131-136.
  24. Klungthong C, Chinnawirotpisan P, Hussem K, Phonpakobsin T, Manasatienkij W, Ajariyakhajorn C, Rungrojcharoenkit K, Gibbons RV, Jarman RG. The impact of primer and probe-template mismatches on the sensitivity of pandemic influenza A/H1N1/2009 virus detection by real-time RT-PCR. J Clin Virol 2010;48:91-95.
  25. Stadhouders R, Pas SD, Anber J, Voermans J, Mes TH, Schutten M. The effect of primer-template mismatches on the detection and quantification of nucleic acids using the 5' nuclease assay. J Mol Diagn 2010;12:109-117.
  26. Reusken C, Broberg EK, Haagmans B, Meijer A, Corman VM, Papa A, Charrel R, Drosten C, Koopmans M, Leitmeyer K. Laboratory readiness and response for novel coronavirus (2019-nCoV) in expert laboratories in 30 EU/EEA countries, January 2020. Eurosurveillance 2020;25:2000082.
  27. Dahmani CA, Khaldi F, Derouiche W, Benyagoub N, Ghizlene Amara Zenati L, Hamidi W, Bencheikh N. Comparison between RT-qPCR and LAMP methods for a rapid COVID-19 diagnosis in an Algerian sample. [Internet]. Rapid Antigen Testing IntechOpen. 2023. Available from: http://dx.doi.org/10.5772/intechopen.1001116

Files

Share

How to cite

Statistics