Tags

Type your tag names separated by a space and hit enter

The establishment of reference sequence for SARS-CoV-2 and variation analysis.
J Med Virol. 2020 06; 92(6):667-674.JM

Abstract

Starting around December 2019, an epidemic of pneumonia, which was named COVID-19 by the World Health Organization, broke out in Wuhan, China, and is spreading throughout the world. A new coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses was soon found to be the cause. At present, the sensitivity of clinical nucleic acid detection is limited, and it is still unclear whether it is related to genetic variation. In this study, we retrieved 95 full-length genomic sequences of SARAS-CoV-2 strains from the National Center for Biotechnology Information and GISAID databases, established the reference sequence by conducting multiple sequence alignment and phylogenetic analyses, and analyzed sequence variations along the SARS-CoV-2 genome. The homology among all viral strains was generally high, among them, 99.99% (99.91%-100%) at the nucleotide level and 99.99% (99.79%-100%) at the amino acid level. Although overall variation in open-reading frame (ORF) regions is low, 13 variation sites in 1a, 1b, S, 3a, M, 8, and N regions were identified, among which positions nt28144 in ORF 8 and nt8782 in ORF 1a showed mutation rate of 30.53% (29/95) and 29.47% (28/95), respectively. These findings suggested that there may be selective mutations in SARS-COV-2, and it is necessary to avoid certain regions when designing primers and probes. Establishment of the reference sequence for SARS-CoV-2 could benefit not only biological study of this virus but also diagnosis, clinical monitoring and intervention of SARS-CoV-2 infection in the future.

Authors+Show Affiliations

Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China. Institute of Clinical Virology, The Second Hospital of Anhui Medical University, Hefei, China. Department of Infectious Diseases, The Affiliated Anqing Hospital of Anhui Medical University, Anqing, China.Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China. Institute of Clinical Virology, The Second Hospital of Anhui Medical University, Hefei, China.Institute of Clinical Virology, The Second Hospital of Anhui Medical University, Hefei, China.Institute of Clinical Virology, The Second Hospital of Anhui Medical University, Hefei, China.Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China. Institute of Clinical Virology, The Second Hospital of Anhui Medical University, Hefei, China.Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China. Institute of Clinical Virology, The Second Hospital of Anhui Medical University, Hefei, China.Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China. Institute of Clinical Virology, The Second Hospital of Anhui Medical University, Hefei, China. Anhui Provincial Laboratory of Inflammatory and Immunity Disease, Anhui Medical University, Hefei, China.

Pub Type(s)

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

Language

eng

PubMed ID

32167180

Citation

Wang, Changtai, et al. "The Establishment of Reference Sequence for SARS-CoV-2 and Variation Analysis." Journal of Medical Virology, vol. 92, no. 6, 2020, pp. 667-674.
Wang C, Liu Z, Chen Z, et al. The establishment of reference sequence for SARS-CoV-2 and variation analysis. J Med Virol. 2020;92(6):667-674.
Wang, C., Liu, Z., Chen, Z., Huang, X., Xu, M., He, T., & Zhang, Z. (2020). The establishment of reference sequence for SARS-CoV-2 and variation analysis. Journal of Medical Virology, 92(6), 667-674. https://doi.org/10.1002/jmv.25762
Wang C, et al. The Establishment of Reference Sequence for SARS-CoV-2 and Variation Analysis. J Med Virol. 2020;92(6):667-674. PubMed PMID: 32167180.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The establishment of reference sequence for SARS-CoV-2 and variation analysis. AU - Wang,Changtai, AU - Liu,Zhongping, AU - Chen,Zixiang, AU - Huang,Xin, AU - Xu,Mengyuan, AU - He,Tengfei, AU - Zhang,Zhenhua, Y1 - 2020/03/20/ PY - 2020/02/28/received PY - 2020/03/10/accepted PY - 2020/3/14/pubmed PY - 2020/7/1/medline PY - 2020/3/14/entrez KW - SARS-CoV-2 KW - homology KW - nucleotide KW - reference sequence KW - variation SP - 667 EP - 674 JF - Journal of medical virology JO - J. Med. Virol. VL - 92 IS - 6 N2 - Starting around December 2019, an epidemic of pneumonia, which was named COVID-19 by the World Health Organization, broke out in Wuhan, China, and is spreading throughout the world. A new coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses was soon found to be the cause. At present, the sensitivity of clinical nucleic acid detection is limited, and it is still unclear whether it is related to genetic variation. In this study, we retrieved 95 full-length genomic sequences of SARAS-CoV-2 strains from the National Center for Biotechnology Information and GISAID databases, established the reference sequence by conducting multiple sequence alignment and phylogenetic analyses, and analyzed sequence variations along the SARS-CoV-2 genome. The homology among all viral strains was generally high, among them, 99.99% (99.91%-100%) at the nucleotide level and 99.99% (99.79%-100%) at the amino acid level. Although overall variation in open-reading frame (ORF) regions is low, 13 variation sites in 1a, 1b, S, 3a, M, 8, and N regions were identified, among which positions nt28144 in ORF 8 and nt8782 in ORF 1a showed mutation rate of 30.53% (29/95) and 29.47% (28/95), respectively. These findings suggested that there may be selective mutations in SARS-COV-2, and it is necessary to avoid certain regions when designing primers and probes. Establishment of the reference sequence for SARS-CoV-2 could benefit not only biological study of this virus but also diagnosis, clinical monitoring and intervention of SARS-CoV-2 infection in the future. SN - 1096-9071 UR - https://www.unboundmedicine.com/medline/citation/32167180/The_establishment_of_reference_sequence_for_SARS_CoV_2_and_variation_analysis_ L2 - https://doi.org/10.1002/jmv.25762 DB - PRIME DP - Unbound Medicine ER -