• Zohreh Fattahi, Marzieh Mohseni, Maryam Beheshtian, Ali Jafarpour, Khadijeh Jalalvand, Fatemeh Keshavarzi, Hanieh Behravan, Fatemeh Ghodratpour, Farzane Zare Ashrafi, Marzieh Kalhor, Maryam Azad, Mahdieh Koshki, Azam Ghaziasadi, Mohamad Soveyzi, Alireza Abdollahi, Seyed Jalal Kiani, Angila Ataei-Pirkooh, Iman Rezaeiazhar, Farah Bokharaei-Salim, Mohammad Reza Haghshenas, Farhang Babamahmoodi, Zakiye Mokhames, Alireza Soleimani, Zohreh Elahi, Masood Ziaee, Davod Javanmard, Shokouh Ghafari, Akram Ezani, Alireza Ansari Moghaddam, Fariba Shahraki-Sanavi, Seyed Mohammad Hashemi Shahri, Azarakhsh Azaran, Farid Yousefi, Afagh Moattari, Mohsen Moghadami, Hamed Fakhim, Behrooz Ataei, Elahe Nasri, Vahdat Poortahmasebi, Mojtaba Varshochi, Ali Mojtahedi, Farid Jalilian, Mohammad Khazeni, Abdolvahab Moradi, Alijan Tabarraei, Ahmad Piroozmand, Yousef Yahyapour, Masoumeh Bayani, Fatemeh Tavangar, Mahmood Yaghoubi, Fariba Keramat, Mahsa Tavakoli, Tahmineh Jalali, Mohammad Hassan Pouriayevali, Mostafa Salehi-Vaziri, Hamid Reza Khorram Khorshid, Reza Najafipour, Reza Malekzadeh, Kimia Kahrizi, Seyed Mohammad Jazayeri, and Hossein Najmabadi.
• Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
• Arch Iran Med. 2022 Aug 1; 25 (8): 508522508-522.

BackgroundComplete 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.MethodsWe provided 319 SARS-CoV-2 whole-genome sequences used to monitor circulating lineages in March 2020-May 2021 time interval.ResultsThe 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.ConclusionIn 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.© 2022 The Author(s). This is an open-access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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