Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective

Miao, Miao; Clercq, Erik De; Li, Guangdi

doi:10.3390/biomedicines9040412

Cited by 25 publications

(22 citation statements)

References 78 publications

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“…The 19B clade did not rise in Iran, while in February 2021 resurgence of this clade was reported in some countries (dominated by A.23.1, A.27 and, A.2.5 lineages) (Murall et al 2021). From mid-September 2020 onward, the pandemic was dominated by 20E clade, while we detected 20B dominancy, which is more similar to the pandemic in Asia, in which 20B was the leading clade in January (Miao et al 2021).…”

Section: Discussionmentioning

confidence: 52%

“…The observed difference is largely caused by the different time intervals of the two cohorts rather than the distinct genetic diversity of SARS-CoV-2 in Iran compared to the world. Miao et al investigated 260,673 sequences between December 2019-12 January 2021, before the dominancy of B.1.1.7 lineage in the world (Miao et al 2021).…”

Section: Resultsmentioning

confidence: 99%

“…Today; over one year after the declaration of the COVID-19 pandemic by WHO, genome surveillance projects are frequently performed in all countries with the intention of tracking the spread of SARS-CoV-2 variants (Miao et al 2021). The current study is the report of complete genome sequencing of 369 SARS-CoV-2 viral isolates of the Iranian outbreak from March 2020 till the end of May 2021.…”

Section: Discussionmentioning

confidence: 99%

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

Fattahi

Mohseni

Beheshtian

et al. 2021

Preprint

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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.

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Section: Discussionmentioning

confidence: 52%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

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

Fattahi

Mohseni

Beheshtian

et al. 2021

Preprint

View full text Add to dashboard Cite

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“…The same results were observed in a similar study on SARS-CoV-2 in a Canadian population conducted by Zhang et al [ 47 ]. In addition, a recent analysis performed on 260,673 whole-genome sequences to study the selection pressure among the coding genes highlighted the rarity of positive selection in SARS-CoV-2 protein-coding genes [ 48 ].…”

Section: Discussionmentioning

confidence: 99%

The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect

Zeghbib

Somogyi

Zana

et al. 2021

Viruses

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To explore the SARS-CoV-2 pandemic in Algeria, a dataset comprising ninety-five genomes originating from SARS-CoV-2 sampled from Algeria and other countries worldwide, from 24 December 2019, through 4 March 2021, was thoroughly examined. While performing a multi-component analysis regarding the Algerian outbreak, the toolkit of phylogenetic, phylogeographic, haplotype, and genomic analysis were effectively implemented. We estimated the Time to the Most Recent Common Ancestor (TMRCA) in reference to the Algerian pandemic and highlighted the multiple introductions of the disease and the missing data depicted in the transmission loop. In addition, we emphasized the significant role played by local and international travels in disease dissemination. Most importantly, we unveiled mutational patterns, the effect of unique mutations on corresponding proteins, and the relatedness regarding the Algerian sequences to other sequences worldwide. Our results revealed individual amino-acid replacements such as the deleterious replacement A23T in the orf3a gene in Algeria_EPI_ISL_418241. Additionally, a connection between Algeria_EPI_ISL_420037 and sequences originating from the USA was observed through a USA characteristic amino-acid replacement T1004I in the nsp3 gene, found in the aforementioned Algerian sequence. Similarly, successful tracing could be established, such as Algeria/G37318-8849/2020|EPI_ISL_766863, which was imported from Saudi Arabia during the pilgrimage. Lastly, we assessed the Algerian mitigation measures regarding disease containment using statistical analyses.

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“…The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged in Wuhan, China, is an RNA virus that belongs to the genus Betacoronavirus , in the family Coronaviridae ( 1 ). Like most RNA viruses, SARS-CoV-2 is expected to display a relatively high rate of genetic mutations, which may influence viral transmission and pathogenesis, enable escape from host defenses, and negatively affect the efficacy of vaccines and molecular diagnostic tools ( 2 ). Thus, enhancing genomic capacity is important to investigate the transmission and to monitor the evolution and mutational patterns of SARS-CoV-2 in this country.…”

Section: Announcementmentioning

confidence: 99%

Whole-Genome Sequences of SARS-CoV-2 Isolates from Ethiopian Patients

Alemayehu

Adnew

Alemu

et al. 2021

Microbiol Resour Announc

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Three complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Ethiopian patients were compared with deposited global genomes. Two genomes belonged to genetic group 20A/B.1/GH, and the other belonged to genetic group 20A/B.1.480/GH. Enhancing genomic capacity is important to investigate the transmission and to monitor the evolution and mutational patterns of SARS-CoV-2 in this country.

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Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective

Cited by 25 publications

References 78 publications

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

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

The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect

Whole-Genome Sequences of SARS-CoV-2 Isolates from Ethiopian Patients

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