Disease waves of SARS-CoV-2 in Iran closely mirror global pandemic trends

Abstract

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.

Analysis of Whole-Genome Sequencing of SARS-CoV-2 Reveals Recurrent Mutations among Iranian Patients

“…Previous genomics analysis in Iran reported six mutations that have a frequency of more than 50% of the sequences, including D614G, P323L, R203K, G204R, F105F, and C241T [28]. In the United States, top mutations were reported as F106F, S76S, L7L, T85I, P323L, D614G, Q57H, L84S, Y541C, P504L, S24L, R203K, and G204R [29].…”

“…On 03/31/2020, the first spike mutations in D614 were detected in Iran and Figure 7C). Previous study reported that the D614G mutation was first detected in Iran in May 2020 [28]. S477N and S477G strengthen the binding of the SARS-COV-2 spike with the hACE2 receptor [75].…”

“…A previous study showed that three spike mutations, D138Y, S477N, and D614G, co-occur in B.1.1. * lineages [28]. First amino acid substitution in T478 was detected on 01/31/2020 worldwide, and then in August 2021, the mutation in T478 dramatically increased in the following months.…”

“…The dates that were D614G first seen in China and Germany was on 24 January 2020 and was rare before March 2020 but increased steadily over time and now become one of the most prevalent mutations among all the continents [70, 71]. The first case with the D614G mutation in Iran was reported on 1 May 2020 and become major spike mutation after 1 September 2020 [28]. D614G is the second-highest frequency in the United States and has been associated with increased viral replication in primary human upper airway tissues [72].…”

“…According to our results Q19E (54.9%), D3G (37.5%), I73M (15.5%) and A63T (6.9%), were the most common mutations in our sample. (Figure 2 and supplementary 3).The I73M is the characteristic mutation of B.1.1.413 lineage [28] and the I82T highly prevalent mutation in 176 countries/territories, and one of the top mutations worldwide [88].…”