SARS‐CoV‐2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions

• DOI: 10.1111/tbed.14104
• Publication Date: 2021-04-09T12:02:44Z
• Authors: Zohreh Fattahi; Marzieh Mohseni; Khadijeh Jalalvand; Fatemeh Aghakhani...; Azam Ghaziasadi; Fatemeh Keshavarzi; Jila Yavarian; Ali Jafarpour; Seyedeh Elham Mor...; Fatemeh Ghodratpour; Hanieh Behravan; Mohammad Khazeni; Seyed Amir Momeni; Issa Jahanzad; Abdolvahab Moradi; Alijan Tabarraei; Sadegh Ali Azimi; Ebrahim Kord; Seyed Mohammad Ha...; Azarakhsh Azaran; Farid Yousefi; Zakiye Mokhames; Alireza Soleimani; Shokouh Ghafari; Masood Ziaee; Shahram Habibzadeh; Farhad Jeddi; Azar Hadadi; Alireza Abdollahi; Gholam Abbas Kaydani; Saber Soltani; Talat Mokhtari‐Azad; Reza Najafipour; Reza Malekzadeh; Kimia Kahrizi; Seyed Mohammad Ja...; Hossein Najmabadi
• Keywords: 0301 basic medicine; 03 medical and health sciences; SARS-CoV-2; Animals; COVID-19; Genome, Viral; Iran; Phylogeny; Disease Outbreaks; 3. Good health

The SARS-CoV-2 virus has been rapidly spreading globally since December 2019, triggering a pandemic, soon after its emergence. While Iran was among the first countries confronted with rapid spread of virus in February 2020, no real-time SARS-CoV-2 whole-genome tracking in early phase of outbreak was performed in the country. To address this issue, we provided 50 whole-genome sequences of viral isolates ascertained from different geographical locations in Iran during March-July 2020. The corresponding analysis on origins, transmission dynamics and genetic diversity of SARS-CoV-2 virus, represented at least two introductions of the virus into the country, constructing two major clusters defined as B.4 and B.1*. The first entry of the virus might have occurred around very late 2019/early 2020, as suggested by the time to the most recent common ancestor, followed by a rapid community transmission that led to dominancy of B.4 lineage in early epidemic till the end of June. Gradually, reduction in dominancy of B.4 occurred possibly as a result of other entries of the virus, followed by surge of B.1* lineages, as of mid-May. Remarkably, variation tracking of the virus indicated the increase in frequency of D614G mutation, along with B.1* lineages, which showed continuity till October 2020. The increase in frequency of D614G mutation and B.1* lineages from mid-May onwards predicts a rapid viral transmission that may push the country into a critical health situation followed by a considerable change in composition of viral lineages circulating in the country.