Disease waves of SARS-CoV-2 in Iran closely mirror global pandemic
trends
Authors: Fattahi Zohreh , Mohseni Marzieh , Beheshtian Maryam , Jafarpour Ali , Jalalvand Khadijeh , Keshavarzi Fatemeh , Behravan Hanieh , Ghodratpour Fatemeh , Ashrafi Farzane Zare , Kalhor Marzieh , Azad Maryam , Koshki Mahdieh , Ghaziasadi Azam , Soveyzi Mohamad , Abdollahi Alireza , Kiani Seyed Jalal , Ataei-Pirkooh Angila , Rezaeiazhar Iman , Bokharaei-Salim Farah , Haghshenas Mohammad Reza , Babamahmoodi Farhang , Mokhames Zakiye , Soleimani Alireza , Elahi Zohreh , Ziaee Masood , Javanmard Davod , Ghafari Shokouh , Ezani Akram , AnsariMoghaddam Alireza , Shahraki-Sanavi Fariba , HashemiShahri Seyed Mohammad , Azaran Azarakhsh , Yousefi Farid , Moattari Afagh , Moghadami Mohsen , Fakhim Hamed , Ataei Behrooz , Nasri Elahe , Poortahmasebi Vahdat , Varshochi Mojtaba , Mojtahedi Ali , Jalilian Farid , khazeni Mohammad , Moradi Abdolvahab , Tabarraei Alijan , Piroozmand Ahmad , Yahyapour Yousef , Bayani Masoumeh , Tavangar Fatemeh , Yaghoubi Mahmood , Keramat Fariba , Tavakoli Mahsa , Jalali Tahmineh , Pouriayevali Mohammad Hassan , Salehi-Vaziri Mostafa , Khorram Khorshid Hamid Reza , Najafipour Reza , Malekzadeh Reza , Kahrizi Kimia , Jazayeri Seyed Mohammad , Najmabadi Hossein 
Published: February 2022

SARS-CoV-2 genome surveillance projects provide a good measure of
transmission and monitor the circulating SARS-CoV-2 variants at regional and
global scales. Iran is one of the most affected countries still involved with
the virus circulating in at least five significant disease waves, as of
September 2021. Complete genome sequencing of 50 viral isolates in an early
phase of outbreak in Iran, shed light on the origins and circulating lineages at
that time. As part of a genomic surveillance program, we provided an additional
319 complete genomes from October 2020 onwards. The current study is the report
of complete SARS-CoV-2 genome sequences of Iran in the March 2020-May 2021 time
interval. We aimed to characterize the genetic diversity of SARS-CoV-2 in Iran
over one year.

Overall, 35 different lineages and 8 clades were detected. Temporal dynamics
of the prominent SARS-CoV-2 clades/lineages circulating in Iran is comparable to
the global perspective and introduces 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) clades,
dominating second, third and fourth disease waves, respectively. We observed a
mixture of circulating 20A (B.1.36), 20B (B.1.1.413), 20I (B.1.1.7) clades in
winter 2021, paralleled in a diminishing manner for 20A/20B and a growing rise
for 20I, eventually prompting the 4th outbreak peak.
Furthermore, our study provides evidence on the entry of the Delta variant in
April 2021, leading to the 5th disease wave in summer
2021.

Three lineages are highlighted as hallmarks of SARS-CoV-2 outbreak in Iran;
B4, dominating early periods of the epidemic, B.1.1.413 (specific B.1.1 lineage
carrying a combination of [D138Y-S477N-D614G] spike mutations) in October
2020-February 2021, and the co-occurrence of [I100T-L699I] spike mutations in
half of B.1.1.7 sequences mediating the fourth peak.

Continuous monthly monitoring of SARS-CoV-2 genome mutations led to the
detection of 1577 distinct nucleotide mutations, in which the top recurrent
mutations were D614G, P323L, R203K/G204R, 3037C>T, and 241C>T; the
renowned combination of mutations in G and GH clades. The most frequent spike
mutation is D614G followed by 13 other frequent mutations based on the prominent
circulating lineages; B.1.1.7 (H69_V70del, Y144del, N501Y, A570D, P681H, T716I,
S982A, D1118H, I100T, and L699I), B.1.1.413 (D138Y, S477N) and B.1.36
(I210del).

In brief, mutation surveillance in this study provided a real-time
comprehensive picture of the SARS-CoV-2 mutation profile in Iran, which is
beneficial for evaluating the magnitude of the epidemic and assessment of
vaccine and therapeutic efficiency in this population.