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A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions.
OMICS. 2021 02; 25(2):123-128.O

Abstract

The novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is causing an unprecedented pandemic, threatening planetary health, society, and economy. Genomic surveillance continues to be a critical effort toward tracking the virus and containing its spread, and more genomes from diverse geographical areas and different time points are needed to provide an appropriate representation of the virus evolution. In this study, we report the successful assembly of one single gapless, unambiguous contiguous sequence representing the complete viral genome from a nasopharyngeal swab of an infected health care worker in Cairo, Egypt. The sequence has all typical features of SARS-CoV-2 genomes, with no protein-disrupting mutations. However, three mutations are worth highlighting and future tracking: a synonymous mutation causing a rare spike S813I variation and two less frequent ones leading to an A41V variation in NSP3, encoded by ORF1a (ORF1a A895V), and a Q677H variation in the spike protein. Both affected proteins, S and NSP3, are relevant to vaccine and drug development. Although the genome, named CU_S3, belongs to the prevalent global genotype, marked by the D614G spike variation, the combined variations in the spike proteins and ORF1a do not co-occur in any of the 197,000 genomes reported to date. Future studies will assess the biological, pathogenic, and epidemiological implications of this set of genetic variations. This line of research is needed to inform vaccine and therapeutic innovation to stem the COVID-19 pandemic.

Authors+Show Affiliations

Clinical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.Clinical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt. Cairo University Pediatric Hospital, Cairo, Egypt.Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt. Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

33253058

Citation

Soliman, May S., et al. "A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions." Omics : a Journal of Integrative Biology, vol. 25, no. 2, 2021, pp. 123-128.
Soliman MS, AbdelFattah M, Aman SMN, et al. A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions. OMICS. 2021;25(2):123-128.
Soliman, M. S., AbdelFattah, M., Aman, S. M. N., Ibrahim, L. M., & Aziz, R. K. (2021). A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions. Omics : a Journal of Integrative Biology, 25(2), 123-128. https://doi.org/10.1089/omi.2020.0194
Soliman MS, et al. A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions. OMICS. 2021;25(2):123-128. PubMed PMID: 33253058.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions. AU - Soliman,May S, AU - AbdelFattah,May, AU - Aman,Soad M N, AU - Ibrahim,Lamyaa M, AU - Aziz,Ramy K, Y1 - 2020/11/30/ PY - 2020/12/1/pubmed PY - 2021/3/2/medline PY - 2020/11/30/entrez KW - COVID-19 KW - genomic epidemiology KW - high-throughput sequencing KW - pandemic KW - replicase KW - spike protein SP - 123 EP - 128 JF - Omics : a journal of integrative biology JO - OMICS VL - 25 IS - 2 N2 - The novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is causing an unprecedented pandemic, threatening planetary health, society, and economy. Genomic surveillance continues to be a critical effort toward tracking the virus and containing its spread, and more genomes from diverse geographical areas and different time points are needed to provide an appropriate representation of the virus evolution. In this study, we report the successful assembly of one single gapless, unambiguous contiguous sequence representing the complete viral genome from a nasopharyngeal swab of an infected health care worker in Cairo, Egypt. The sequence has all typical features of SARS-CoV-2 genomes, with no protein-disrupting mutations. However, three mutations are worth highlighting and future tracking: a synonymous mutation causing a rare spike S813I variation and two less frequent ones leading to an A41V variation in NSP3, encoded by ORF1a (ORF1a A895V), and a Q677H variation in the spike protein. Both affected proteins, S and NSP3, are relevant to vaccine and drug development. Although the genome, named CU_S3, belongs to the prevalent global genotype, marked by the D614G spike variation, the combined variations in the spike proteins and ORF1a do not co-occur in any of the 197,000 genomes reported to date. Future studies will assess the biological, pathogenic, and epidemiological implications of this set of genetic variations. This line of research is needed to inform vaccine and therapeutic innovation to stem the COVID-19 pandemic. SN - 1557-8100 UR - https://www.unboundmedicine.com/medline/citation/33253058/A_Gapless_Unambiguous_RNA_Metagenome_Assembled_Genome_Sequence_of_a_Unique_SARS_CoV_2_Variant_Encoding_Spike_S813I_and_ORF1a_A859V_Substitutions_ L2 - https://www.liebertpub.com/doi/10.1089/omi.2020.0194?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub=pubmed DB - PRIME DP - Unbound Medicine ER -