The design of Indonesian SARS‐CoV‐2 primers based on phylogenomic analysis of the SARS‐CoV‐2 clades

Tsania Taskia Nabila; Ata Rofita Wasiati; Afif Pranaya Jati; Annisa Khumaira

doi:10.22146/ijbiotech.66854

The design of Indonesian SARS‐CoV‐2 primers based on phylogenomic analysis of the SARS‐CoV‐2 clades

https://doi.org/10.22146/ijbiotech.66854

Tsania Taskia Nabila⁽¹⁾, Ata Rofita Wasiati⁽²⁾, Afif Pranaya Jati⁽³⁾, Annisa Khumaira^(4*)

(1) Biotechnology Study Program, Faculty of Science and Technology, Universitas ‘Aisyiyah Yogyakarta, Jl. Ringroad Barat No.63, Nogotirto, Gamping, Sleman, Daerah Istimewa Yogyakarta 55592, Indonesia
(2) Biotechnology Study Program, Faculty of Science and Technology, Universitas ‘Aisyiyah Yogyakarta, Jl. Ringroad Barat No.63, Nogotirto, Gamping, Sleman, Daerah Istimewa Yogyakarta 55592, Indonesia
(3) Masyarakat Bioinformatika dan Biodiversitas Indonesia (MABBI), Ruang 613, Lantai 6, Program Studi Bioteknologi, Universitas Esa Unggul, Jl. Arjuna Utara No. 9, Jakarta Barat 11510, Indonesia
(4) Biotechnology Study Program, Faculty of Science and Technology, Universitas ‘Aisyiyah Yogyakarta, Jl. Ringroad Barat No.63, Nogotirto, Gamping, Sleman, Daerah Istimewa Yogyakarta 55592, Indonesia
(*) Corresponding Author

Abstract

Molecular detection needs to be augmented for COVID‐19 detection in Indonesia using the PCR method with primer‐based gene analysis. This is necessary because the RNA of the SARS‐CoV‐2 virus, the causative infectious agent of the pandemic, has been mutated. Therefore, this study aimed to develop a primer design for determining SARS‐CoV‐2 clades in Indonesia using phylogenomic analysis. Data were obtained from 38 GISAID (Global Initiative on Sharing All Influenza Data) viruses and the relationships were analyzed using maximum likelihood (ML) phylogenomic analysis with a substitution model of generalized time‐reversible (GTR) to construct the tree topology. The results showed that the five types of SARS‐CoVs‐2 clades in Indonesia were L, G, GH, GR, and O. It also indicated that the GH region had the highest rate of clade at 50%, with the S clade affecting its formation. Furthermore, the genome sequences of the GH type used to design its primer were based on three genes, namely RdRp, S, and N. The RdRp and N genes were found to be conserved and hardy mutants, while the S gene occurred repeatedly. Several previous studies have stated that the designed primers produced missense mutations compared to another in silico. Therefore, three sets of primers were achieved from the GC contents and clamps, Tm range, and structural secondary indicator standards.

Keywords

maximum likelihood method; phylogenomic analysis; primer design; SARS‐CoV‐2

Full Text:

PDF

References

Ansori ANM, Kharisma VD, Antonius Y, Tacharina MR, Rantam FA. 2020. Immunobioinformatics analysis and phylogenetic tree construction of severe acute respiratory syndrome coronavirus 2 (SARSCoV2) in Indonesia: spike glycoprotein gene. J. Teknol. Lab. 9(1). doi:10.29238/teknolabjournal.v9i1.221.

Arenas M. 2015. Trends in substitution models of molecular evolution. Front. Genet. 6(OCT). doi:10.3389/fgene.2015.00319.

Boopathi S, Poma AB, Kolandaivel P. 2020. Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment. doi:10.1080/07391102.2020.1758788.

Bustin SA, Nolan T. 2020. RTQPCR testing of SARSCOV2: A primer. Int. J. Mol. Sci. 21(8). doi:10.3390/ijms21083004.

Davi MJP, Jeronimo SM, Lima JP, Lanza DC. 2021. Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARSCoV2). Sci. Rep. 11(1). doi:10.1038/s41598021918179.

Dhar A, Minin V. 2016. Maximum Likelihood Phylogenetic Inference. Oxford: Academic Press. doi:https://doi.org/10.1016/B978012800049 6.002079. URL https://www.sciencedirect.com/scie nce/article/pii/B9780128000496002079.

Djalante R, Lassa J, Setiamarga D, Sudjatma A, Indrawan M, Haryanto B, Mahfud C, Sinapoy MS, Djalante S, Rafliana I, Gunawan LA, Surtiari GAK, Warsilah H. 2020. Review and analysis of current responses to COVID19 in Indonesia: Period of January to March 2020. Prog. Disaster Sci. 6. doi:10.1016/j.pdisas.2020.100091.

Eaaswarkhanth M, Al Madhoun A, AlMulla F. 2020. Could the D614G substitution in the SARSCoV 2 spike (S) protein be associated with higher COVID19 mortality? Int. J. Infect. Dis. 96. doi:10.1016/j.ijid.2020.05.071.

Githinji G, de Laurent ZR, Mohammed KS, Omuoyo DO, Macharia PM, Morobe JM, Otieno E, Kinyanjui SM, Agweyu A, Maitha E, Kitole B, Suleiman T, Mwakinangu M, Nyambu J, Otieno J, Salim B, Kasera K, Kiiru J, Aman R, Barasa E, Warimwe G, Bejon P, Tsofa B, OcholaOyier LI, Nokes DJ, Agoti CN. 2021. Tracking the introduction and spread of SARSCoV2 in coastal Kenya. Nat. Commun. 12(1). doi:10.1038/s4146702125137x.

Guindon S, Lethiec F, Duroux P, Gascuel O. 2005. PHYML Online A web server for fast maximum likelihoodbased phylogenetic inference. Nucleic Acids Res. 33(SUPPL. 2). doi:10.1093/nar/gki352.

Hamed SM, Elkhatib WF, Khairalla AS, Noreddin AM. 2021. Global dynamics of SARSCoV2 clades and their relation to COVID19 epidemiology. Sci. Rep. 11(1). doi:10.1038/s4159802187713x.

Islam MT, Alam ARU, Sakib N, Hasan MS, Chakrovarty T, Tawyabur M, Islam OK, AlEmran HM, Jahid MIK, Anwar Hossain M. 2021. A rapid and costeffective multiplex ARMSPCR method for the simultaneous genotyping of the circulating SARSCoV2 phylogenetic clades. J. Med. Virol. 93(5). doi:10.1002/jmv.26818.

Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, Angyal A, Brown RL, Carrilero L, Green LR, Groves DC, Johnson KJ, Keeley AJ, Lindsey BB, Parsons PJ, Raza M, RowlandJones S, Smith N, Tucker RM, Wang D, Wyles MD, McDanal C, Perez LG, Tang H, MoonWalker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. 2020. Tracking Changes in SARSCoV2 Spike: Evidence that D614G Increases Infectivity of the COVID19 Virus. Cell 182(4). doi:10.1016/j.cell.2020.06.043.

Kuo L, Masters PS. 2003. The Small Envelope Protein E Is Not Essential for Murine Coronavirus Replication. J. Virol. 77(8). doi:10.1128/jvi.77.8.45974608.2003.

Li D, Zhang J, Li J. 2020. Primer design for quantitative realtime PCR for the emerging Coronavirus SARSCoV2. Theranostics 10(16):7150– 7162. doi:10.7150/thno.47649.

Makarenkov V, Kevorkov D, Legendre P. 2006. Phylogenetic Network Construction Approaches, volume 6. Elsevier. doi:https://doi.org/10.1016/S1874 5334(06)800067.

Mercatelli D, Giorgi FM. 2020. Geographic and Genomic Distribution of SARSCoV2 Mutations. Front. Microbiol. 11. doi:10.3389/fmicb.2020.01800.

PereiraGómez M, Fajardo Á, Echeverría N, LópezTort F, Perbolianachis P, Costábile A, Aldunate F, Moreno P, Moratorio G. 2021. Evaluation of SYBR Green real time PCR for detecting SARSCoV2 from clinical samples. J. Virol. Methods 289. doi:10.1016/j.jviromet.2020.114035.

Sanjuán R, DomingoCalap P. 2016. Mechanisms of viral mutation. doi:10.1007/s0001801622996. S

cohy A, Anantharajah A, Bodéus M, KabambaMukadi B, Verroken A, RodriguezVillalobos H. 2020. Low performance of rapid antigen detection test as frontline testing for COVID19 diagnosis. J. Clin. Virol. 129. doi:10.1016/j.jcv.2020.104455.

Selberg AG, Gaucher EA, Liberles DA. 2021. Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond. doi:10.1007/s00239021099931.

Shereen MA, Khan S, Kazmi A, Bashir N, Siddique R. 2020. Covid19 infection: origin, transmission, and characteristics of human coronaviruses. Https://doi.org/10.1016/j.jare.2020.03.005 65.

World Health Organization (WHO).2020. Advice on the use of masks in the c. J. Adv. Res. 24. Tang YW, Schmitz JE, Persing DH, Stratton CW. 2020. Laboratory diagnosis of COVID19: Current issues and challenges. doi:10.1128/JCM.0051220.

Tavaré S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Turista DDR, Islamy A, Kharisma VD, Ansori ANM. 2020. Distribution of COVID19 and phylogenetic tree construction of sarsCoV 2 in Indonesia. J. Pure Appl. Microbiol. 14. doi:10.22207/JPAM.14.SPL1.42.

Umair M, Ikram A, Salman M, Khurshid A, Alam M, Badar N, Suleman R, Tahir F, Sharif S, Montgomery J, Whitmer S, Klena J. 2021. Wholegenome sequencing of SARSCoV2 reveals the detection of G614 variant in Pakistan. PLoS One 16(3 March). doi:10.1371/journal.pone.0248371.

Van de Peer Y, Salemi M. 2012. Phylogenetic inference based on distance methods. Cambridge University Press. doi:10.1017/cbo9780511819049.007.

VegaMagaña N, SánchezSánchez R, HernándezBello J, VenancioLanderos AA, PeñaRodríguez M, VegaZepeda RA, GalindoOrnelas B, DíazSánchez M, GarcíaChagollán M, MacedoOjeda G, GarcíaGonzález OP, MuñozValle JF. 2021. RTqPCR Assays for Rapid Detection of the N501Y, 6970del, K417N, and E484K SARSCoV2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Front. Cell. Infect. Microbiol. 11. doi:10.3389/fcimb.2021.672562.

Venkataraman S, Prasad BV, Selvarajan R. 2018. RNA dependent RNA polymerases: Insights from structure, function and evolution. doi:10.3390/v10020076.

Wang Y, Kang H, Liu X, Tong Z. 2020. Combination of RTqPCR testing and clinical features for diagnosis of COVID19 facilitates management of SARSCoV2 outbreak. doi:10.1002/jmv.25721.

Wurm T, Chen H, Hodgson T, Britton P, Brooks G, Hiscox JA. 2001. Localization to the Nucleolus Is a Common Feature of Coronavirus Nucleoproteins, and the Protein May Disrupt Host Cell Division. J. Virol. 75(19). doi:10.1128/jvi.75.19.93459356.2001.

DOI: https://doi.org/10.22146/ijbiotech.66854