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Implementation of an In-House Platform for Rapid Screening of Sars-Cov-2 Genome Variations Publisher Pubmed



Ashrafi FZ1 ; Mohseni M1, 2 ; Beheshtian M1, 2 ; Fattahi Z1, 2 ; Ghodratpour F1 ; Keshavarzi F1 ; Behravan H1 ; Kalhor M1 ; Jalalvand K1 ; Azad M2 ; Koshki M2 ; Jafarpour A3, 4 ; Ghaziasadi A3 ; Abdollahi A5 Show All Authors
Authors
  1. Ashrafi FZ1
  2. Mohseni M1, 2
  3. Beheshtian M1, 2
  4. Fattahi Z1, 2
  5. Ghodratpour F1
  6. Keshavarzi F1
  7. Behravan H1
  8. Kalhor M1
  9. Jalalvand K1
  10. Azad M2
  11. Koshki M2
  12. Jafarpour A3, 4
  13. Ghaziasadi A3
  14. Abdollahi A5
  15. Kiani SJ6
  16. Ataeipirkooh A6
  17. Azhar IR3
  18. Bokharaeisalim F6
  19. Haghshenas MR7
  20. Babamahmoodi F7
  21. Mokhames Z8
  22. Soleimani A9
  23. Ziaee M10
  24. Javanmard D10
  25. Ghafari S10
  26. Ezani A11
  27. Moghaddam AA12
  28. Shahrakisanavi F12
  29. Shahri SMH13
  30. Azaran A14
  31. Yousefi F15
  32. Moattari A16
  33. Moghadami M17
  34. Fakhim H18
  35. Ataei B18
  36. Nasri E18
  37. Poortahmasebi V19
  38. Varshochi M20
  39. Mojtahedi A21
  40. Jalilian F22
  41. Khazeni M23
  42. Moradi A24
  43. Tabarraei A24
  44. Piroozmand A25
  45. Yahyapour Y26
  46. Bayani M26
  47. Aboofazeli A3
  48. Ghafari P3
  49. Keramat F27
  50. Tavakoli M28
  51. Jalali T28, 29
  52. Pouriayevali MH28, 29
  53. Salehivaziri M28, 29
  54. Khorshid HRK1
  55. Najafipour R1, 30
  56. Malekzadeh R31
  57. Kahrizi K1
  58. Jazayeri SM3
  59. Najmabadi H1, 2
Show Affiliations
Authors Affiliations
  1. 1. Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
  2. 2. Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
  3. 3. Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
  4. 4. Gerash Amir-al-Momenin Medical and Educational Center, Gerash University of Medical Sciences, Gerash, Iran
  5. 5. Department of Pathology, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Iran
  6. 6. Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
  7. 7. Department of Medical Microbiology, Antimicrobial Resistance Research Center, Communicable Diseases Institute, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
  8. 8. Department of Molecular Diagnostic, Emam Ali Educational and Therapeutic Center, Alborz University of Medical Sciences, Karaj, Iran
  9. 9. Department of Infectious Diseases, Imam Ali hospital, Alborz University of Medical Sciences, Karaj, Iran
  10. 10. Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
  11. 11. Qazvin Deputy of Treatment Reference Laboratory, Qazvin University of Medical Sciences, Qazvin, Iran
  12. 12. Health Promotion Research Center, Zahedan University of Medical Science, Zahedan, Iran
  13. 13. Infection Disease and Tropical Medicine Research Center, Zahedan University of Medical Science, Zahedan, Iran
  14. 14. Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
  15. 15. Department of Infectious Diseases, School of Medicine, Razi Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
  16. 16. Department of Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
  17. 17. Health policy research center, Shiraz University of medical sciences, Shiraz, Iran
  18. 18. Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
  19. 19. Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
  20. 20. Infectious and Tropical Disease Research Center, Tabriz University of Medical Science, Tabriz, Iran
  21. 21. Microbiology Department, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
  22. 22. Department of Medical Virology, Faculty of Medicine, Hamadan University of Medical sciences, Hamadan, Iran
  23. 23. Booali lab, Molecular & Virology Diagnostic Section, Qom, Iran
  24. 24. Golestan University of Medical Sciences, Gorgan, Iran
  25. 25. Department of Microbiology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
  26. 26. Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran
  27. 27. Brucellosis Research Center, Hamedan University of Medical Science, Hamadan, Iran
  28. 28. COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran
  29. 29. Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
  30. 30. Cell and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
  31. 31. Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran

Source: Archives of Iranian Medicine Published:2023


Abstract

Background: Global real-time monitoring of SARS-CoV-2 variants is crucial to controlling the COVID-19 outbreak. The purpose of this study was to set up a Sanger-based platform for massive SARS-CoV-2 variant tracking in laboratories in low-resource settings. Methods: We used nested RT-PCR assay, Sanger sequencing and lineage assignment for 930-bp of the SARS-CoV-2 spike gene, which harbors specific variants of concern (VOCs) mutations. We set up our platform by comparing its results with whole genome sequencing (WGS) data on 137 SARS-CoV-2 positive samples. Then, we applied it on 1028 samples from March-September 2021. Results: In total, 125 out of 137 samples showed 91.24% concordance in mutation detection. In lineage assignment, 123 out of 137 samples demonstrated 89.78% concordance, 65 of which were assigned as VOCs and showed 100% concordance. Of 1028 samples screened by our in-house method, 78 distinct mutations were detected. The most common mutations were: S:D614G (21.91%), S:P681R (12.19%), S:L452R (12.15%), S:T478K (12.15%), S:N501Y (8.91%), S:A570D (8.89%), S:P681H (8.89%), S:T716I (8.74%), S:L699I (3.50%) and S:S477N (0.28%). Of 1028 samples, 980 were attributed as VOCs, which include the Delta (B.1.617.2) and Alpha (B.1.1.7) variants. Conclusion: Our proposed in-house Sanger-based assay for SARS-CoV-2 lineage assignment is an accessible strategy in countries with poor infrastructure facilities. It can be applied in the rapid tracking of SARS-CoV-2 VOCs in the SARS-CoV-2 pandemic. © 2023 Academy of Medical Sciences of I.R. Iran. All rights reserved.
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