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Variant analysis of SARS-CoV-2 genomes in the Middle East.
Bindayna, Khalid Mubarak; Crinion, Shane.
  • Bindayna KM; Department of Microbiology, Immunology, and Infectious Diseases, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain. Electronic address: bindayna@agu.edu.bh.
  • Crinion S; School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, University Road, Galway, Ireland. Electronic address: s.crinion1@nuigalway.ie.
Microb Pathog ; 153: 104741, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-1080796
Preprint
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ABSTRACT

BACKGROUND:

Coronavirus (COVID-19) was introduced into society in late 2019 and has now reached over 88 million cases and 1.9 million deaths. The Middle East has a death toll of ~80,000 and over 35000 of these are in Iran, which has over 1.2 million confirmed cases. We expect that Iranian cases caused outbreaks in the neighbouring countries and that variant mapping and phylogenetic analysis can be used to prove this. We also aim to analyse the variants of severe acute respiratory syndrome coronavirus-2 (SARS -CoV-2) to characterise the common genome variants and provide useful data in the global effort to prevent further spread of COVID-19.

METHODS:

The approach uses bioinformatics approaches including multiple sequence alignment, variant calling and annotation and phylogenetic analysis to identify the genomic variants found in the region. The approach uses 122 samples from the 13 countries of the Middle East sourced from the Global Initiative on Sharing All Influenza Data (GISAID).

FINDINGS:

We identified 2200 distinct genome variants including 129 downstream gene variants, 298 frame shift variants, 789 missense variants, 1 start lost, 13 start gained, 1 stop lost, 249 synonymous variants and 720 upstream gene variants. The most common, high impact variants were 10818delTinsG, 2772delCinsC, 14159delCinsC and 2789delAinsA. These high impact variant ultimately results in 36 number of mutations on spike glycoprotein. Variant alignment and phylogenetic tree generation indicates that samples from Iran likely introduced COVID-19 to the rest of the Middle East.

INTERPRETATION:

The phylogenetic and variant analysis provides unique insight into mutation types in genomes. Initial introduction of COVID-19 was most likely due to Iranian transmission. Some countries show evidence of novel mutations and unique strains. Increased time in small populations is likely to contribute to more unique genomes. This study provides more in depth analysis of the variants affecting in the region than any other study.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genetic Variation / Spike Glycoprotein, Coronavirus / SARS-CoV-2 Type of study: Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Country/Region as subject: Asia Language: English Journal: Microb Pathog Journal subject: Communicable Diseases / Microbiology Year: 2021 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genetic Variation / Spike Glycoprotein, Coronavirus / SARS-CoV-2 Type of study: Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Country/Region as subject: Asia Language: English Journal: Microb Pathog Journal subject: Communicable Diseases / Microbiology Year: 2021 Document Type: Article