DOI: https://dx.doi.org/10.18203/2394-6040.ijcmph20214791
Published: 2021-12-27

An overview of the emerging SARS-CoV-2 variants in the Middle East

Areej M. Alsyamy, Taraheeb K. Alajmi, Ibrahim F. Alamri, Basmah F. Alamri, Waseem M. Mahmoud, Abdulrahman A. Aljohani, Mohammed A. Almutairi, Ibrahim F. Alshaikh, Layali I. Assiri, Asma A. Alhrthialsharif, Hashim Y. Alnami

Abstract


Studying genomic mutations and variants of severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) provides a remarkable insight into the efficacy of the novel treatment and interventional modalities, like vaccines. The Middle East is one of the most burdened countries with COVID-19. Different reports from this region reported various mutations and variants of COVID-19. Therefore, we aim to provide an overview of the emerging SARS-CoV-2 variants in the region. Evidence from studies conducted in the Middle East and North Africa (MENA) region shows a great shifting to D614G from D614 variants of SARS-CoV-2 in the region. This is also similar to the patterns reported by other investigations on a worldwide level. In addition, single experiments also reported mutations that were not previously detected elsewhere, and some studies even linked some mutations and specific COVID-19 symptoms. These findings indicate the need to conduct further research in the region to validate the importance of these mutations and relate them with the effectiveness and manufacturing of the different therapeutic and interventional approaches.


Keywords


SARS-CoV-2, Middle East, Variants, Genomes, Phylogeny, COVID-19

Full Text:

PDF

References


Duffy S, Shackelton LA, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants. Nature Reviews Genetics. 2008;9(4):267-76.

Liu YC, Kuo RL, Shih SR. COVID-19: The first documented coronavirus pandemic in history. Biomed J. 2020;43(4):328-33.

Sevajol M, Subissi L, Decroly E, Canard B, Imbert I. Insights into RNA synthesis, capping, and proofreading mechanisms of SARS-coronavirus. Virus Research. 2014;194:90-9.

Fehr AR, Perlman S. Coronaviruses: An Overview of Their Replication and Pathogenesis. In: Maier HJ, Bickerton E, Britton P, editors. Coronaviruses: Methods and Protocols. New York, NY: Springer New York. 2015;1-23.

Gebru AA, Birhanu T, Wendimu E, Ayalew AF, Mulat S, Abasimel HZ, et al. Global burden of COVID-19: Situational analyis and review. Human Antibodies. 2021;29(2):139-48.

Akande OW, Akande TM. COVID-19 pandemic: A global health burden. Nigerian Postgrad Med J. 2020;27(3):147-55.

Mian A, Al-Asad S, Khan S. Mental health burden of COVID-19. Family Practice. 2021;38(2):195-7.

Sallam M, Ababneh NA, Dababseh D, Bakri FG, Mahafzah A. Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Heliyon. 2021;7(1):e06035.

Zekri AN, Mohanad M, Hafez MM, Soliman HK, Hassan ZK, Abouelhoda M, et al. Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Biochimica et biophysica acta Molecular basis of disease. 2021;1867(8):166154.

Cuevas JM, Geller R, Garijo R, López-Aldeguer J, Sanjuán R. Extremely High Mutation Rate of HIV-1 In Vivo. PLoS biology. 2015;13(9):e1002251.

Tang XC, Agnihothram SS, Jiao Y, Stanhope J, Graham RL, Peterson EC, et al. Identification of human neutralizing antibodies against MERS-CoV and their role in virus adaptive evolution. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(19):2018-26.

Bindayna KM, Crinion S. Variant analysis of SARS-CoV-2 strains in Middle Eastern countries. bioRxiv. 2020.

Abou-Hamdan M, Hamze K, Abdel Sater A, Akl H, El-Zein N, Dandache I, et al. Variant analysis of the first Lebanese SARS-CoV-2 isolates. Genomics. 2021;113(1):892-5.

Dos Ramos F, Carrasco M, Doyle T, Brierley I. Programmed -1 ribosomal frameshifting in the SARS coronavirus. Biochemical Society transactions. 2004;32(6):1081-3.

Koyama T, Platt D, Parida L. Variant analysis of SARS-CoV-2 genomes. Bull World Health Organization. 2020;98(7):495.

Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, et al. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med. 2020;18(1):179.

Yao H, Lu X, Chen Q, Xu K, Chen Y, Cheng M, et al. Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo. Cell discovery. 2020;6(1):76.

Benvenuto D, Angeletti S, Giovanetti M, Bianchi M, Pascarella S, Cauda R, et al. Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy. J Infect. 2020;81(1):24-7.

Yin C. Genotyping coronavirus SARS-CoV-2: methods and implications. Genomics. 2020;112(5):3588-96.

Gupta AM, Chakrabarti J, Mandal S. Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Microbes and infection. 2020;22(10):598-607.

Kim S-J, Nguyen V-G, Park Y-H, Park B-K, Chung H-C. A novel synonymous mutation of SARS-CoV-2: is this possible to affect their antigenicity and immunogenicity? Vaccines. 2020;8(2):220.

De Maio N, Walker C, Borges R, Weilguny L, Slodkowicz G, Goldman N. Issues with SARS-CoV-2 sequencing data. 2020. Available at: https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473. Accessed on 24 July 2021.

Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, et al. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell. 2020;182(4):812-27.

Karamouzian M, Madani N. COVID-19 response in the Middle East and north Africa: challenges and paths forward. The Lancet Global Health. 2020;8(7):886-7.

Yang X, Dong N, Chan EW-C, Chen S. Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries. Emerging microbes & infections. 2020;9(1):1287-99.

MacLean OA, Orton RJ, Singer JB, Robertson DL. No evidence for distinct types in the evolution of SARS-CoV-2. Virus Evolution. 2020;6(1):veaa034.

Tang X, Wu C, Li X, Song Y, Yao X, Wu X, et al. On the origin and continuing evolution of SARS-CoV-2. National Science Review. 2020;7(6):1012-23.

Yurkovetskiy L, Pascal KE, Tomkins-Tinch C, Nyalile T, Wang Y, Baum A, et al. SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain. BioRxiv. 2020.

Zhang L, Jackson CB, Mou H, Ojha A, Rangarajan ES, Izard T, et al. The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. BioRxiv. 2020.

Farkas C, Fuentes-Villalobos F, Garrido JL, Haigh J, Barría MI. Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions. Peer J. 2020;8:e9255.

Deng X, Gu W, Federman S, Plessis Ld, Pybus OG, Faria NR, et al. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science. 2020;369(6503):582-7.

Gong Y-N, Tsao K-C, Hsiao M-J, Huang C-G, Huang P-N, Huang P-W, et al. SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Emerging microbes & infections. 2020;9(1):1457-66.

Laamarti M, Kartti S, Alouane T, Laamarti R, Allam L, Ouadghiri M, et al. Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum. bioRxiv. 2020.

Maitra A, Sarkar MC, Raheja H, Biswas NK, Chakraborti S, Singh AK, et al. Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. J Biosci. 2020;45(1):1-18.

Mourier T, Shuaib M, Hala S, Mfarrej S, Alofi F, Naeem R, et al. Saudi Arabian SARS-CoV-2 genomes implicate a mutant Nucleocapsid protein in modulating host interactions and increased viral load in COVID-19 patients. medRxiv. 2021.

Bindayna KM, Crinion S. Variant analysis of SARS-CoV-2 genomes in the Middle East. Microbial Pathogenesis. 2021;153:104741.

Tayoun AA, Loney T, Khansaheb H, Ramaswamy S, Harilal D, Deesi ZO, et al. Multiple early introductions of SARS-CoV-2 into a global travel hub in the Middle East. Sci Rep. 2020;10(1):17720.

Sahin E, Bozdayi G, Yigit S, Muftah H, Dizbay M, Tunccan OG, et al. Genomic characterization of SARS-CoV-2 isolates from patients in Turkey reveals the presence of novel mutations in spike and nsp12 proteins. J Med Virol. 2021;93(10):6016-26.