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

Abstract

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.

Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan

“…However, the whole genome sequences of the first three SARS-CoV-2 samples, collected in March, revealed the presence of B and B.4 lineages in the country. The lineage B.4 was reported to have a major role in the early pandemic in Iran [25]. This supports the hypothesis of an early transmission of the virus to Pakistan most likely from Iran and China, and this is also consistent with the statement of Pakistan's health ministry officials who confirmed the first two cases of COVID-19 on 26 February 2020 from patients who travelled back to Pakistan from Iran.…”

Socio-demographical Profile of 7285 SARS-Cov-2 Positive Early Cases; Comparison with National Four Epidemic Waves

“…We observed two separate trends were seen for Ct ≤ 25 and Ct ≤ 20 for the first and the fourth epidemic peaks, respectively. Previous Iranian data indicated that clade B4 was the dominant clade in the country between March 2019 and May 2020, compatible with the first epidemic wave ( 26 ).…”

SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study)

“…Fattahi, Zohreh, et al genomic sequencing and phylogenetic analysis suggested that SARS‐CoV‐2 entered in late 2019/early 2020 in Iran and circulated among vulnerable patients. The increase in the frequency of D614G mutations and B.1* lineages from mid‐May onwards predicted a rapid viral transmission followed by a considerable change in the composition of viral lineages circulating in the country [ 29 ]. According to the results of our phylogenetic tree ( Fig.…”