1,102
Views
4
CrossRef citations to date
0
Altmetric
Research Paper

Statistical analysis supports UTR (untranslated region) deletion theory in SARS-CoV-2

ORCID Icon, , & ORCID Icon
Pages 1772-1789 | Received 06 May 2022, Accepted 29 Sep 2022, Published online: 10 Oct 2022

References

  • Xiao Y, Torok ME. Taking the right measures to control COVID-19[J]. Lancet Infect Dis. 2020;20(5):523–524.
  • Zhu N, Zhang D, Wang W, et al. A novel coronavirus from patients with pneumonia in China, 2019[J]. N Engl J Med. 2020;382(8):727–733. DOI:10.1056/NEJMoa2001017
  • Wang C, Horby PW, Hayden FG, et al. A novel coronavirus outbreak of global health concern[j]. Lancet. 2020;395(10223):470–473. DOI:10.1016/S0140-6736(20)30185-9
  • Chapman NM, Kim K-S, Drescher KM, et al. 5′ terminal deletions in the genome of a coxsackievirus B2 strain occurred naturally in human heart. Virology. 2008;375(2):480–491. DOI:10.1016/j.virol.2008.02.030
  • Lévêque N, et al. Functional consequences of RNA 5′-terminal deletions on coxsackievirus B3 RNA replication and ribonucleoprotein complex formation. J Virol. 2017;91(16):e00423–17.
  • Hunziker IP, Cornell CT, Lindsay Whitton J Deletions within the 5′ UTR of coxsackievirus B3: consequences for virus translation and replication. Virology. 2007 360(1):120–128.
  • AlMalki WH, Shahid I, Abdalla AN, et al. Consensus small interfering RNA targeted to stem-loops II and III of IRES structure of 5′ UTR effectively inhibits virus replication and translation of HCV sub-genotype 4a isolates from Saudi Arabia[J]. Saudi J Biol Sci. 2021;28(1):1109–1122. DOI:10.1016/j.sjbs.2020.11.041
  • Collier AJ, Tang S, Elliott RM. Translation efficiencies of the 5‘untranslated region from representatives of the six major genotypes of hepatitis C virus using a novel bicistronic reporter assay system[j]. J Gen Virol. 1998;79(10):2359–2366.
  • Tang S, Collier AJ, Elliott RM. Alterations to both the primary and predicted secondary structure of stem-loop IIIc of the hepatitis C virus 1b 5′ untranslated region (5′ UTR) lead to mutants severely defective in translation which cannot be complemented in trans by the wild-type 5′ UTR sequence[j]. J Virol. 1999;73(3):2359–2364.
  • Lin YJ, Zhang X, Wu RC, et al. The 3‘untranslated region of coronavirus RNA is required for subgenomic mRNA transcription from a defective interfering RNA[J]. J Virol. 1996;70(10):7236–7240.
  • Demongeot J, Seligmann H. Covid-19 and miRNA-like inhibition power. Med Hypotheses. 2020;144C:110245.
  • Farkas C, Mella A, Turgeon M, et al. A novel SARS-CoV-2 viral sequence bioinformatic pipeline has found genetic evidence that the viral 3′ untranslated region (UTR) is evolving and generating increased viral diversity. Front Microbiol. 2021;12:665041.
  • Zhang JJ, Huang A L, Shi X L, et al. “Promoter activity of SARS coronavirus 5‘UTR sequence in eukaryotic cells.” Sichuan da xue xue bao. Yi Xue Ban= Journal of Sichuan University: Medical Science Edition. 2006;37(1):5–9.
  • Baldassarre A, Paolini A, Bruno SP, et al. Potential use of noncoding RNAs and innovative therapeutic strategies to target the 5’UTR of SARS-CoV-2. Epigenomics. 2020;12(15):1349–1361. DOI:10.2217/epi-2020-0162
  • Cao S, et al. Post-lockdown SARS-CoV-2 nucleic acid screening in nearly ten million residents of Wuhan, China. Nat Commun. 2020;11(1):1–7.
  • Yu WB, Tang GD, Zhang L, et al. Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2) using whole genomic data[j]. ChinaXiv. 2020;41(3): 247.
  • Fang B, Liu L, Yu X, et al. Genome-wide data inferring the evolution and population demography of the novel pneumonia coronavirus (SARS-CoV-2)[J]. bioRxiv. 2020. https://doi.org/10.1101/2020.03.04.976662
  • Zehender G, Lai A, Bergna A, et al. Genomic characterisation and phylogenetic analysis of sars-cov-2 in Italy[j]. Journal of medical virology. 2020;92(9):1637-1640.
  • Tu YF, Chien CS, Yarmishyn AA, et al. A review of SARS-CoV-2 and the ongoing clinical trials[j]. Int J Mol Sci. 2020;21(7):2657.
  • Al Khatib HA, Benslimane FM, Elbashir IE, et al. Within-host diversity of SARS-CoV-2 in COVID-19 patients with variable disease severities[j]. Front Cell Infect Microbiol. 2020;10:575613.
  • Cevik M, Kuppalli K, Kindrachuk J, et al. Virology, transmission, and pathogenesis of SARS-CoV-2[J]. BMJ. 2020:371. DOI:10.1136/bmj.m3862
  • Rosato AE, Msiha E, Weng B, et al. Rapid detection of the widely circulating B. 1.617. 2 (Delta) SARS-CoV-2 variant[j]. Pathology. 2022;54(3):351–356.
  • Demongeot J, Griette Q, Magal P, et al. Modelling vaccine efficacy for COVID-19 outbreak in New York City. Biology (Basel). 2022;11(3):345.
  • Wang L, Cheng G. Sequence analysis of the emerging SARS‐CoV‐2 variant Omicron in South Africa[J]. J Med Virol. 2022;94(4):1728–1733.
  • Yang T, Shen K, He S, et al. CovidNet: to bring data transparency in the era of COVID-19[J]. arXiv Preprint arXiv. 2005;10948. https://doi.org/10.48550/arXiv.2005.10948
  • Faes C, Abrams S, Van Beckhoven D, et al. Time between symptom onset, hospitalisation and recovery or death: statistical analysis of Belgian COVID-19 patients[j]. Int J Environ Res Public Health. 2020;17(20):7560. DOI:10.3390/ijerph17207560
  • Hawryluk I, Mellan TA, Hoeltgebaum H, et al. Inference of COVID-19 epidemiological distributions from Brazilian hospital data[j]. J Royal Soc Interface. 2020;17(172):20200596. DOI:10.1098/rsif.2020.0596
  • Chakravart L, Laha RG, Roy JW. Handbook of methods of applied statistics. Vol. I: techniques of computation, descriptive methods and statistical inference[j]. 1967;1047–1049.
  • Nagy Á, Pongor S, Győrffy B. Different mutations in SARS-CoV-2 associate with severe and mild outcome[j]. Int J Antimicrob Agents. 2021;57(2):106272.
  • Biswas SK, Mudi SR. Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19[J]. Genomics & Informatics. 2020;18(4):e44. DOI:10.5808/GI.2020.18.4.e44.
  • Oulas A, Zanti M, Tomazou M, et al. Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains[j]. PLoS One. 2021;16(1):e0238665. DOI:10.1371/journal.pone.0238665
  • Majumdar P, Niyogi S. Orf3a mutation associated with higher mortality rate in SARS-CoV-2 infection[j]. Epidemiology & Infection. 2020;e262:148. https://doi.org/10.1017/S0950268820002599
  • Voss JD, Skarzynski M, McAuley EM, et al. Variants in SARS-CoV-2 associated with mild or severe outcome[j]. Evol Med Public Health. 2021;9(1):267–275. DOI:10.1093/emph/eoab019
  • Toyoshima Y, Nemoto K, Matsumoto S, et al. SARS-CoV-2 genomic variations associated with mortality rate of COVID-19[J]. J Hum Genet. 2020;65(12):1075–1082. DOI:10.1038/s10038-020-0808-9
  • Volz E, Hill V, McCrone JT, et al. Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity[j]. Cell. 2021;184(1):64–75. e11.
  • Zhang L, Jackson CB, Mou H, et al. SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity[j]. Nat Commun. 2020;11(1):1–9. DOI:10.1038/s41467-020-19808-4
  • Hou YJ, Chiba S, Halfmann P, et al. SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo[j]. Science. 2020;370(6523):1464–1468. DOI:10.1126/science.abe8499
  • Hegde S, Tang Z, Zhao J, et al. Inhibition of SARS-CoV-2 by targeting conserved viral RNA structures and sequences[j]. Front Chem. 2021;9:802766.
  • Vankadari N, Jeyasankar NN, Lopes WJ. Structure of the SARS-CoV-2 Nsp1/5′-untranslated region complex and implications for potential therapeutic targets, a vaccine, and virulence[j]. J Phys Chem Lett. 2020;11(22):9659–9668.
  • Escors D, Izeta A, Capiscol C, et al. Transmissible gastroenteritis coronavirus packaging signal is located at the 5′ end of the virus genome[j]. J Virol. 2003;77(14):7890–7902. DOI:10.1128/JVI.77.14.7890-7902.2003
  • Yang D, Leibowitz JL. The structure and functions of coronavirus genomic 3′ and 5′ ends[j]. Virus Res. 2015;206:120–133.
  • Zhao J, Qiu J, Aryal S, et al. The RNA architecture of the SARS-CoV-2 3′-untranslated region[j]. Viruses. 2020;12(12):1473. DOI:10.3390/v12121473
  • Miao Z, Tidu A, Eriani G, et al. Secondary structure of the SARS-CoV-2 5’-UTR[J]. RNA Biol. 2021;18(4):447–456. DOI:10.1080/15476286.2020.1814556
  • Vora SM, Fontana P, Mao T, et al. Targeting stem-loop 1 of the SARS-CoV-2 5′ UTR to suppress viral translation and Nsp1 evasion[j]. Proc Nat Acad Sci. 2022;119(9):e2117198119. DOI:10.1073/pnas.2117198119
  • Narayanan K, Makino S. Interplay between viruses and host mRNA degradation[j]. Biochimica Et Biophysica Acta (BBA)-Gene Regulatory Mechanisms. 2013;1829(6–7):732–741.
  • Wacker A, Weigand JE, Akabayov SR, et al. Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy[j]. Nucleic Acids Res. 2020;48(22):12415–12435. DOI:10.1093/nar/gkaa1013
  • Shu Y, McCauley J. GISAID: global initiative on sharing all influenza data–from vision to reality[j]. Eurosurveillance. 2017;22(13):30494.
  • Hatcher EL, Zhdanov SA, Bao Y, et al. Virus Variation Resource–improved response to emergent viral outbreaks[j]. Nucleic Acids Res. 2017;45(D1):D482–490.
  • Likic V. The Needleman-Wunsch algorithm for sequence alignment[j]. Lecture given at the 7th Melbourne bioinformatics course, Bi021 molecular science and biotechnology institute. University of Melbourne; 2008. pp. 1–46.
  • Spinelli MA, Glidden DV, Gennatas ED, et al. Importance of non-pharmaceutical interventions in lowering the viral inoculum to reduce susceptibility to infection by SARS-CoV-2 and potentially disease severity[j]. Lancet Infect Dis. 2021;21(9):e296–301. DOI:10.1016/S1473-3099(20)30982-8
  • Best K, Barouch DH, Guedj J, et al. Zika virus dynamics: effects of inoculum dose, the innate immune response and viral interference[j]. PLoS Comput Biol. 2021;17(1):e1008564. DOI:10.1371/journal.pcbi.1008564
  • Xu Z, Yang D, Zhang H. Antibody dynamics simulation-theory and application[J]. 2021. https://doi.org/10.21203/rs.3.rs-967878/v1
  • Roy S, Ghosh P. Factors affecting COVID-19 infected and death rates inform lockdown-related policymaking[j]. PLoS One. 2020;15(10):e0241165.
  • Tian T, Zhang J, Hu L, et al. Risk factors associated with mortality of COVID-19 in 3125 counties of the United States[J]. Infect Dis Poverty. 2021;10(1):1–8. DOI:10.1186/s40249-020-00786-0
  • Jabłońska K, Aballéa S, Toumi M. The real-life impact of vaccination on COVID-19 mortality in Europe and Israel[J]. Public Health. 2021;198:230–237.
  • Xu Z, Zeng Q. More or less deadly? A mathematical model that predicts SARS-CoV-2 evolutionary direction[j]. bioRxiv. 2022. https://doi.org/10.1101/2022.03.10.483726
  • Murray CJL, Piot P. The potential future of the COVID-19 pandemic: will SARS-CoV-2 become a recurrent seasonal infection?[j]. JAMA. 2021;325(13):1249–1250.
  • Sabino EC, Buss LF, Carvalho MPS, et al. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence[j]. Lancet. 2021;397(10273):452–455.
  • Poustchi H, Darvishian M, Mohammadi Z, et al. SARS-CoV-2 antibody seroprevalence in the general population and high-risk occupational groups across 18 cities in Iran: a population-based cross-sectional study[j]. Lancet Infect Dis. 2021;21(4):473–481. DOI:10.1016/S1473-3099(20)30858-6
  • Xu Z, Zhang H, Huang Z. A continuous Markov-chain model for the simulation of COVID-19 epidemic dynamics[J]. Biology (Basel). 2022;11(2):190.
  • Xu Z, Zhang H. If we cannot eliminate them, should we tame them? Mathematics underpinning the dose effect of virus infection and its application on covid-19 virulence evolution[j]. medRxiv. 2021. https://doi.org/10.1101/2021.06.30.21259811
  • Panda M, Kalita E, Singh S, et al. MiRNA-SARS-CoV-2 dialogue and prospective anti-COVID-19 therapies. Life Sci. 2022;305:120761.
  • Natarelli L, Parca L, Mazza T, et al. MicroRnas and long non-coding RNAs as potential candidates to target specific motifs of SARS-CoV-2[J]. Noncoding RNA. 2021;7(1):14. DOI:10.3390/ncrna7010014