Zohreh Fattahi
1,2 
, Marzieh Mohseni
1,2, Maryam Beheshtian
1,2, Ali Jafarpour
3,4, Khadijeh Jalalvand
1, Fatemeh Keshavarzi
1, Hanieh Behravan
1, Fatemeh Ghodratpour
1, Farzane Zare Ashrafi
1, Marzieh Kalhor
1, Maryam Azad
2, Mahdieh Koshki
2, Azam Ghaziasadi
3, Mohamad Soveyzi
1, Alireza Abdollahi
5, Seyed Jalal Kiani
6, Angila Ataei-Pirkooh
6, Iman Rezaeiazhar
3, Farah Bokharaei-Salim
6, Mohammad Reza Haghshenas
7, Farhang Babamahmoodi
7, Zakiye Mokhames
8, Alireza Soleimani
9, Zohreh Elahi
1, Masood Ziaee
10, Davod Javanmard
10, Shokouh Ghafari
10, Akram Ezani
11, Alireza Ansari Moghaddam
12, Fariba Shahraki-Sanavi
12, Seyed Mohammad Hashemi Shahri
13, Azarakhsh Azaran
14, Farid Yousefi
15, Afagh Moattari
16, Mohsen Moghadami
17, Hamed Fakhim
18, Behrooz Ataei
18, Elahe Nasri
18, Vahdat Poortahmasebi
19, Mojtaba Varshochi
20, Ali Mojtahedi
21, Farid Jalilian
22, Mohammad Khazeni
23, Abdolvahab Moradi
24, Alijan Tabarraei
24, Ahmad Piroozmand
25, Yousef Yahyapour
26, Masoumeh Bayani
26, Fatemeh Tavangar
27, Mahmood Yaghoubi
28, Fariba Keramat
29, Mahsa Tavakoli
30, Tahmineh Jalali
30,31, Mohammad Hassan Pouriayevali
30,31, Mostafa Salehi-Vaziri
30,31, Hamid Reza Khorram Khorshid
1, Reza Najafipour
1, Reza Malekzadeh
32, Kimia Kahrizi
1, Seyed Mohammad Jazayeri
3, Hossein Najmabadi
1,2* 1 Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
2 Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
3 Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
4 Gerash Amir-al-Momenin Medical and Educational Center, Gerash University of Medical Sciences, Gerash, Iran
5 Department of Pathology, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
6 Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
7 Department of Medical Microbiology, Antimicrobial Resistance Research Center, Communicable Diseases Institute, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
8 Department of Molecular Diagnostic, Emam Ali Educational and Therapeutic Center, Alborz University of Medical Sciences, Karaj, Iran
9 Department of Infectious Diseases, Imam Ali hospital, Alborz University of Medical Sciences, Karaj, Iran
10 Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
11 Qazvin Deputy of Treatment Reference Laboratory, Qazvin University of Medical Sciences, Qazvin, Iran
12 Health Promotion Research Center, Zahedan University of Medical Science, Zahedan, Iran
13 Infection Disease and Tropical Medicine Research Center, Zahedan University of Medical Science, Zahedan, Iran
14 Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
15 Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
16 Department of Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
17 Health Policy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
18 Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
19 Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
20 Infectious and Tropical Disease Research Center, Tabriz University of Medical Science, Tabriz, Iran
21 Microbiology Department, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
22 Department of Medical Virology, Faculty of Medicine, Hamadan University of Medical sciences, Hamadan, Iran
23 Booali Lab, Molecular & Virology Diagnostic Section, Qom, Iran
24 Golestan University of Medical Sciences, Gorgan, Iran
25 Department of Microbiology, School Of Medicine, Kashan University of Medical Sciences, Kashan, Iran
26 Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran
27 Iranian Blood Transfusion Research Center, High Institute for Education and Research in Transfusion Medicine, Tehran, Iran
28 Aramesh Pathology & Genetics laboratory, Tehran, Iran
29 Brucellosis Research Center, Hamedan University of Medical Science, Hamadan, Iran
30 COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran
31 Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
32 Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
Abstract
Background: Complete SARS-CoV-2 genome sequencing in the early phase of the outbreak in Iran showed two independent viral entries. Subsequently, as part of a genome surveillance project, we aimed to characterize the genetic diversity of SARS-CoV-2 in Iran over one year after emerging.
Methods: We provided 319 SARS-CoV-2 whole-genome sequences used to monitor circulating lineages in March 2020-May 2021 time interval.
Results: The temporal dynamics of major SARS-CoV-2 clades/lineages circulating in Iran is comparable to the global perspective and represent the 19A clade (B.4) dominating the first disease wave, followed by 20A (B.1.36), 20B (B.1.1.413), 20I (B.1.1.7), leading the second, third and fourth waves, respectively. We observed a mixture of circulating B.1.36, B.1.1.413, B.1.1.7 lineages in winter 2021, paralleled in a fading manner for B.1.36/B.1.1.413 and a growing rise for B.1.1.7, prompting the fourth outbreak. Entry of the Delta variant, leading to the fifth disease wave in summer 2021, was detected in April 2021. This study highlights three lineages as hallmarks of the SARS-CoV-2 outbreak in Iran; B4, dominating early periods of the epidemic, B.1.1.413 (B.1.1 with the combination of [D138Y-S477N-D614G] spike mutations) as a characterizing lineage in Iran, and the co-occurrence of [I100T-L699I] spike mutations in half of B.1.1.7 sequences mediating the fourth peak. It also designates the renowned combination of G and GR clades’ mutations as the top recurrent mutations.
Conclusion: In brief, we provided a real-time and comprehensive picture of the SARS-CoV-2 genetic diversity in Iran and shed light on the SARS-CoV-2 transmission and circulation on the regional scale.