Document Type : Original Article

Author

Medical Laboratory Science Department College of Medicals and Applied Sciences Charmo University 46023 Chamchamal/ Sulaimani

Abstract

The COVID-19 is an on-going viral pandemic that has been affecting the public health, routine life and global economy. The disease is caused by a novel strain of coronavirus, called SARS-CoV-2 virus. The COVID-19 outbreak has been reporting in Kurdistan region of Iraq since March 2020. However, few studies investigated the epidemiology of COVID-19 and SARS CoV-2 virus in the region. This study aims at investigating the epidemiological situations of COVID-19 and SARS-CoV-2 variants in Kurdistan region over a year of the pandemic. The results revealed that the prevalence of COVID-19 is 1.9% in the region and is still in parallel to the neighbouring countries and the entire world. The mortality is 59 per 100,000 populations that may be related with age, as 25 % of the patients are older than 50 years old, and underlying health conditions of the patients might be another reason. Meanwhile, the recovery rate is high (90.5%), suggesting a standard medical management of COVID-19 in the region. It was observed that males comprise the greater number of COVID-19 patients. Like other countries, Kurdistan region passed through two waves of COVID-19 and currently tackling the third wave. On the other hand, the investigated spike proteins of nine isolates of SARS-CoV-2 in Kurdistan showed five isolates with single (D614G) mutation and four isolates with multiple amino acid substitutions (A348S, T478K and D614G), (L452R, E583D and D614G) and (N501Y, A570D and D614G), of which A348S, L452R and T478K and N501Y are in the receptor binding domain (RBD). Interestingly, all the isolates in Kurdistan contained D614G mutation. The D614G mutation alone and in combination with other mutations makes the SARS-CoV-2 virus more infectious and transmissible, so virulent variants of the virus is currently circulating and might be the cause of third wave of COVID-19 in Kurdistan region. The detection of N501Y and A570D mutations indicate the circulation of the UK variant of concern in Kurdistan region. Moreover, the results showed that the altered amino acids (A348S, L452R and T478K and N501Y) in the RBD of spike protein are located in the predicted B-cell epitopes. This could possibly reduce the sensitivity of some neutralizing antibodies, produced after infection with the previous variants or after vaccination. This and future investigations of COVID-19 epidemiology and SARS-CoV-2 variants definitely provide insights to the Kurdistan health officials to evaluate, control and predict the course of COVID-19 pandemic and to order the right version of vaccine.

Keywords

  1. References

    1. Guan, W.-j., et al., Clinical Characteristics of Coronavirus Disease 2019 in China. New England Journal of Medicine, 2020. 382(18): p. 1708-1720.
    2. Zhu, N., et al., A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med, 2020. 382(8): p. 727-733.
    3. World Health Organization ''Coronavirus Disease 2019 (COVID-19) Situation Report−51''. https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200311-sitrep-51-covid-19.pdf?sfvrsn=1ba62e57_10, 2020.
    4. World Health Organization '' Coronavirus (COVID-19) Dashboard''. https://covid19.who.int/, 2021.
    5. Backer, J.A., D. Klinkenberg, and J. Wallinga, Incubation period of 2019 novel coronavirus (2019-nCoV) infections among travellers from Wuhan, China, 20-28 January 2020. Euro Surveill, 2020. 25(5).
    6. Li, Q., et al., Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia. New England Journal of Medicine, 2020. 382.
    7. Cao, X., COVID-19: immunopathology and its implications for therapy. Nat Rev Immunol, 2020. 20(5): p. 269-270.
    8. Chan, J.F. and K.H. Kok, Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. 2020. 9(1): p. 221-236.
    9. Ahmed, S.F., A.A. Quadeer, and M.R. McKay, Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies. Viruses, 2020. 12(3).
    10. Jeyanathan, M., et al., Immunological considerations for COVID-19 vaccine strategies. 2020. 20(10): p. 615-632.
    11. Wrapp, D. and N. Wang, Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. 2020. 367(6483): p. 1260-1263.
    12. Li, Q., et al., The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Cell, 2020. 182(5): p. 1284-1294.e9.
    13. Shin, M.D., et al., COVID-19 vaccine development and a potential nanomaterial path forward. Nature nanotechnology, 2020. 15(8): p. 646-655.
    14. Wu, F., et al., Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications. medRxiv, 2020: p. 2020.03.30.20047365.
    15. Duffy, S., Why are RNA virus mutation rates so damn high? PLoS Biol, 2018. 16(8): p. e3000003.
    16. Lauring, A.S. and R. Andino, Quasispecies theory and the behavior of RNA viruses. PLoS Pathog, 2010. 6(7): p. e1001005.
    17. Khailany, R.A., M. Safdar, and M. Ozaslan, Genomic characterization of a novel SARS-CoV-2. Gene Rep, 2020. 19: p. 100682.
    18. Reid, A.H. and J.K. Taubenberger, The origin of the 1918 pandemic influenza virus: a continuing enigma. J Gen Virol, 2003. 84(Pt 9): p. 2285-2292.
    19. Carrat, F. and A. Flahault, Influenza vaccine: the challenge of antigenic drift. Vaccine, 2007. 25(39-40): p. 6852-62.
    20. Wise, J., Covid-19: New coronavirus variant is identified in UK. BMJ, 2020. 371: p. m4857.
    21. Chand, M., et al., Investigation of novel SARS-COV-2 variant: Variant of Concern 202012/01. Technical breifing 1. Public Health England. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/959438/Technical_Briefing_VOC_SH_NJL2_SH2.pdf, 2020.
    22. World Health Organization ''Novel Coronavirus (2019-nCoV) Situation Report−1''. https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200121-sitrep-1-2019-ncov.pdf?sfvrsn=20a99c10_4, 2020.
    23. Kurdistan Regional Government. Situation Update on Coronavirus (COVID-19) Dashboard. https://gov.krd/coronavirus-en/situation-update/, 2021.
    24. Current World Population, Worldometers https://www.worldometers.info/world-population/, 2021.
    25. National Centre for Biotechnology Information (NCBI). https://www.ncbi.nlm.nih.gov/, 2021.
    26. Jespersen, M.C., et al., BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res, 2017. 45(W1): p. W24-w29.
    27. Kurdistan Region Statistics Office, Ministry of Planning, Kurdistan Regional Government-Iraq. http://www.krso.net/Default.aspx?page=article&id=12206&l=1, 2020.
    28. Carroll, L., Prevalence, in Encyclopedia of Behavioral Medicine, M.D. Gellman and J.R. Turner, Editors. 2013, Springer New York: New York, NY. p. 1530-1531.
    29. Dana, S., et al., Factors Contributing to the Containment of the COVID-19 in Kurdistan Region of Iraq. Frontiers in Emergency Medicine, 2020. 4(2s).
    30. Aziz, P.Y., et al., The strategy for controlling COVID-19 in Kurdistan Regional Government (KRG)/Iraq: Identification, epidemiology, transmission, treatment, and recovery. International Journal of Surgery Open, 2020. 25: p. 41-46.
    31. Becerra-Flores, M. and T. Cardozo, SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate. 2020. 74(8): p. e13525.
    32. Ramzi, Z.S., Epidemiological and Clinical Characteristics of COVID-19 Patients in Kurdistan Region/Iraq. Annals of the Romanian Society for Cell Biology, 2021. 25(1): p. 2068-2075.
    33. Goyal, P., et al., Clinical Characteristics of Covid-19 in New York City. 2020. 382(24): p. 2372-2374.
    34. Al-Jaf, S.M.A. and S.S. Niranji, Rapid detection of SARS CoV-2 N501Y mutation in clinical samples. medRxiv, 2021: p. 2021.04.17.21255656.
    35. Challen, R., et al., Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study. BMJ, 2021. 372: p. n579.
    36. Davies, N.G., et al., Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Nature, 2021. 593(7858): p. 270-274.
    37. Demographic Survey: Kurdistan Region of Iraq. https://reliefweb.int/sites/reliefweb.int/files/resources/KRSO_IOM_UNFPA_Demographic_Survey_Kurdistan_Region_of_Iraq.pdf, 2018.
    38. Onder, G., G. Rezza, and S. Brusaferro, Case-Fatality Rate and Characteristics of Patients Dying in Relation to COVID-19 in Italy. Jama, 2020. 323(18): p. 1775-1776.
    39. Shim, E., et al., Transmission potential and severity of COVID-19 in South Korea. Int J Infect Dis, 2020. 93: p. 339-344.
    40. Bwire, G.M., Coronavirus: Why Men are More Vulnerable to Covid-19 Than Women? SN comprehensive clinical medicine, 2020: p. 1-3.
    41. Ali, K.M., H.M. Tawfeeq, and H.M. Rostam, COVID-19 Second Spike as an Aftermath of the Sudden Restrictions Ease: Kurdistan Region of Iraq as an Example. Passer Journal, 2020. 2(2): p. 57-61.
    42. Yurkovetskiy, L., et al., Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Cell, 2020. 183(3): p. 739-751.e8.
    43. Zhu, Z., et al., Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies. Proceedings of the National Academy of Sciences, 2007. 104(29): p. 12123-12128.
    44. Lau, E.H.Y., et al., Neutralizing antibody titres in SARS-CoV-2 infections. Nature Communications, 2021. 12(1): p. 63.
    45. Bruni, M., et al., Persistence of Anti-SARS-CoV-2 Antibodies in Non-Hospitalized COVID-19 Convalescent Health Care Workers. 2020. 9(10).
    46. Al-Jaf, S.M.A., S.S. Niranji, and Z.H. Mahmood, Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. medRxiv, 2021: p. 2021.04.12.21255337.
    47. Plante, J.A., et al., Spike mutation D614G alters SARS-CoV-2 fitness. Nature, 2020.
    48. Aktas, E., Bioinformatic Analysis Reveals That Some Mutations May Affect On Both Spike Structure Damage and Ligand Binding Site. bioRxiv, 2020: p. 2020.08.10.244632.
    49. Al-Rashedi, N.A.M., et al., Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq. 2021. 10(4).
    50. Frampton, D., et al., 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. The Lancet Infectious Diseases, 2021.
    51. Peng, J., et al., Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. medRxiv : the preprint server for health sciences, 2021: p. 2021.03.01.21252705.
    52. Cherian, S., et al., Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India. bioRxiv, 2021: p. 2021.04.22.440932.
    53. Wang, R., et al., Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Communications Biology, 2021. 4(1): p. 228.
    54. Sharma, S., et al., Emergence and expansion of highly infectious spike:D614G mutant SARS-CoV-2 in central India. bioRxiv, 2020: p. 2020.09.15.297846.
    55. Banerjee, R., et al., Spike protein mutational landscape in India: Could Muller’s ratchet be a future game-changer for COVID-19? bioRxiv, 2020: p. 2020.08.18.255570.
    56. Wang, R., et al., Characterizing SARS-CoV-2 mutations in the United States. Research square, 2020: p. rs.3.rs-49671.
    57. Garcia-Beltran, W.F., et al., Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell, 2021. 184(9): p. 2372-2383.e9.
    58. El-Manzalawy, Y. and V. Honavar, Recent advances in B-cell epitope prediction methods. Immunome Res, 2010. 6 Suppl 2(Suppl 2): p. S2.
    59. Liu, Z., et al., Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Cell Host Microbe, 2021. 29(3): p. 477-488.e4.
    60. Koyama, T., et al., Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. Pathogens, 2020. 9(5): p. 324.
    61. Grifoni, A., et al., A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2. Cell Host Microbe, 2020. 27(4): p. 671-680.e2.