Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Microbiology Resource Announcements
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
Genome Sequences

Mutation Profile of SARS-CoV-2 Genome Sequences Originating from Eight Israeli Patient Isolates

Galia Zaide, Inbar Cohen-Gihon, Ofir Israeli, Dana Stein, Ohad Shifman, Shay Weiss, Irit Simon, Orly Laskar, Adi Beth-Din, Anat Zvi
John J. Dennehy, Editor
Galia Zaide
aDepartment of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Galia Zaide
Inbar Cohen-Gihon
aDepartment of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ofir Israeli
aDepartment of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Dana Stein
aDepartment of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ohad Shifman
aDepartment of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shay Weiss
bDepartment of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Irit Simon
cDepartment of Biotechnology, Israel Institute for Biological Research, Ness-Ziona, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Orly Laskar
bDepartment of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adi Beth-Din
aDepartment of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Anat Zvi
aDepartment of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Anat Zvi
John J. Dennehy
Queens College
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.01387-20
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

ABSTRACT

We report the genome sequences and the identification of genetic variations in eight clinical samples of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Samples were collected from nasopharyngeal swabs of symptomatic and asymptomatic individuals from five care homes for elderly and infirm persons in Israel. The sequences obtained are valuable, as they carry a newly reported nonsynonymous substitution located within the nucleoprotein open reading frame.

ANNOUNCEMENT

Shortly after a severe acute respiratory syndrome emerged in Wuhan, China, in December 2019 (1, 2), a new Betacoronavirus strain of the Coronaviridae family named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the etiological agent of a disease that was later termed coronavirus disease 19 (COVID-19) (2, 3). In this report, we describe the sequencing of eight SARS-CoV-2 samples obtained from specimens from five care homes for elderly and infirm persons in Israel. This study is in line with the ethical statement of the associate director general of the Israeli Ministry of Health. The individuals were initially identified as positive for COVID-19 by reverse transcriptase quantitative PCR (RT-PCR) and exhibited low cycle threshold (CT) values ranging from 12.8 to 16.8, implying a high viral load. Partial clinical information indicated that at least 2 of the 8 samples (i.e., EPI_ISL_594157 and EPI_ISL_594158) originated from asymptomatic individuals.

Samples were collected directly from swabs, and RNA was extracted with a QIAamp viral RNA minikit (Qiagen) according to the manufacturer’s protocol, using 60 µl of AVE buffer for elution. A SMARTer stranded total RNA-Seq pico input mammalian v2 kit (TaKaRa) was used for library construction prior to sequencing on a MiSeq instrument (Illumina). Whole-genome, paired-end sequencing was conducted in a duplex or triplex format with a read length of 150 nucleotides.

FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc) with default settings was used for quality control of the data. Trimming and removal of low-quality reads were performed using Trim Galore! v0.6.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with default settings. Bowtie 2 (4) with default parameters was used for filtering of the results and for mapping the filtered reads against the reference Wuhan strain (GenBank accession number NC_045512). Reads mapped to SARS-CoV-2 were used as input data for the SPAdes assembler v3.13.0 (5) or the DNAStar software (SeqMan NGen v17.0; DNAStar, Madison, WI), resulting in a single contig for each sample. The genomic features of the samples are summarized in Table 1. Variant calling was performed using the SAMtools software package (6) with default parameters; a variant quality score cutoff of 100 was applied for all samples. A phylogenetic analysis generated using Nextstrain (7), rooted relative to the early samples from Wuhan, revealed that two of the eight samples (i.e., EPI_ISL_594155 and EPI_ISL_594156) belong to clade 20B, while the rest belong to clade 20C.

View this table:
  • View inline
  • View popup
  • Download powerpoint
TABLE 1

Genome features of eight SARS-CoV-2 clinical samples

The variant calling process revealed a total of 52 unique single-nucleotide polymorphism (SNP) replacements. A total of 31 substitutions were nonsynonymous, 4 of which mapped to the Spike coding region; 18 substitutions were of the synonymous type, and the remaining 3 substitutions occurred in noncoding regions (Fig. 1). The eight samples share one common mutation in an intergenic region (position 241, C to T) and two common mutations in coding regions (positions 23403, A to G, and 14408, C to T), resulting in the well-documented D614G substitution and the P323L replacement, respectively (Fig. 1). Apart from the abundant D614G replacement, six other nonsynonymous abundant replacements found in this study (i.e., T85I, L37F, S25L, P323L, A320V, and Q57H; Fig. 1) were previously reported as a result of hot spot mutations (8–10).

FIG 1
  • Open in new tab
  • Download powerpoint
FIG 1

Mutations detected in the SARS-CoV-2 sequences generated in this study. The reference base was retrieved from the reference Wuhan strain (GenBank accession number NC_045512). Samples are named according to the isolate feature in the corresponding GenBank record (see Table 1).

While most of the nonsynonymous replacements were previously reported (11), the A50S substitution (located in the nucleocapsid protein) identified in the EPI_ISL_594161 sample, was not documented before (GISAID [12, 13], as of November 2020).

Although several papers documented a list of viral factors that are correlated with COVID-19 severity (9, 14–16), there is still more to it than meets the eye. Thus, mapping and identification of new mutations may contribute to a better understanding of the viral factors related to clinical outcomes of the disease.

Data availability.The genome sequences have been deposited at the GISAID EpiCoV coronavirus SARS-CoV-2 platform database under the identifiers EPI_ISL_594155, EPI_ISL_594156, EPI_ISL_594157, EPI_ISL_594158, EPI_ISL_594159, EPI_ISL_594160, EPI_ISL_594161, and EPI_ISL_594162 and in the NCBI GenBank database under the accession numbers MW228070, MW194121, MW201576, MW227568, MW237708, MW201577, MW193889, and MW201578. The raw reads have been submitted to the NCBI Sequence Read Archive under the study reference number PRJNA672811.

ACKNOWLEDGMENT

We thank Emanuelle Mamroud for fruitful discussions and support throughout the project.

FOOTNOTES

    • Received 3 December 2020.
    • Accepted 10 December 2020.
    • Published 7 January 2021.
  • Copyright © 2021 Zaide et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Huang C,
    2. Wang Y,
    3. Li X,
    4. Ren L,
    5. Zhao J,
    6. Hu Y,
    7. Zhang L,
    8. Fan G,
    9. Xu J,
    10. Gu X,
    11. Cheng Z,
    12. Yu T,
    13. Xia J,
    14. Wei Y,
    15. Wu W,
    16. Xie X,
    17. Yin W,
    18. Li H,
    19. Liu M,
    20. Xiao Y,
    21. Gao H,
    22. Guo L,
    23. Xie J,
    24. Wang G,
    25. Jiang R,
    26. Gao Z,
    27. Jin Q,
    28. Wang J,
    29. Cao B
    . 2020. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 395:497–506. doi:10.1016/S0140-6736(20)30183-5.
    OpenUrlCrossRefPubMed
  2. 2.↵
    1. Zhu N,
    2. Zhang D,
    3. Wang W,
    4. Li X,
    5. Yang B,
    6. Song J,
    7. Zhao X,
    8. Huang B,
    9. Shi W,
    10. Lu R,
    11. Niu P,
    12. Zhan F,
    13. Ma X,
    14. Wang D,
    15. Xu W,
    16. Wu G,
    17. Gao GF,
    18. Tan W, China Novel Coronavirus Investigation, Research Team
    . 2020. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 382:727–733. doi:10.1056/NEJMoa2001017.
    OpenUrlCrossRefPubMed
  3. 3.↵
    1. Zhou P,
    2. Yang XL,
    3. Wang XG,
    4. Hu B,
    5. Zhang L,
    6. Zhang W,
    7. Si HR,
    8. Zhu Y,
    9. Li B,
    10. Huang CL,
    11. Chen HD,
    12. Chen J,
    13. Luo Y,
    14. Guo H,
    15. Jiang RD,
    16. Liu MQ,
    17. Chen Y,
    18. Shen XR,
    19. Wang X,
    20. Zheng XS,
    21. Zhao K,
    22. Chen QJ,
    23. Deng F,
    24. Liu LL,
    25. Yan B,
    26. Zhan FX,
    27. Wang YY,
    28. Xiao GF,
    29. Shi ZL
    . 2020. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579:270–273. doi:10.1038/s41586-020-2012-7.
    OpenUrlCrossRefPubMed
  4. 4.↵
    1. Langmead B,
    2. Salzberg SL
    . 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. doi:10.1038/nmeth.1923.
    OpenUrlCrossRefPubMedWeb of Science
  5. 5.↵
    1. Bankevich A,
    2. Nurk S,
    3. Antipov D,
    4. Gurevich AA,
    5. Dvorkin M,
    6. Kulikov AS,
    7. Lesin VM,
    8. Nikolenko SI,
    9. Pham S,
    10. Prjibelski AD,
    11. Pyshkin AV,
    12. Sirotkin AV,
    13. Vyahhi N,
    14. Tesler G,
    15. Alekseyev MA,
    16. Pevzner PA
    . 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:10.1089/cmb.2012.0021.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Li H,
    2. Handsaker B,
    3. Wysoker A,
    4. Fennell T,
    5. Ruan J,
    6. Homer N,
    7. Marth G,
    8. Abecasis G,
    9. Durbin R, Genome Project Data Processing Subgroup
    . 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. doi:10.1093/bioinformatics/btp352.
    OpenUrlCrossRefPubMedWeb of Science
  7. 7.↵
    1. Hadfield J,
    2. Megill C,
    3. Bell SM,
    4. Huddleston J,
    5. Potter B,
    6. Callender C,
    7. Sagulenko P,
    8. Bedford T,
    9. Neher RA
    . 2018. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 34:4121–4123. doi:10.1093/bioinformatics/bty407.
    OpenUrlCrossRefPubMed
  8. 8.↵
    1. Alouane T,
    2. Laamarti M,
    3. Essabbar A,
    4. Hakmi M,
    5. Bouricha EM,
    6. Chemao-Elfihri MW,
    7. Kartti S,
    8. Boumajdi N,
    9. Bendani H,
    10. Laamrti R,
    11. Ghrifi F,
    12. Allam L,
    13. Aanniz T,
    14. Ouadghiri M,
    15. El Hafidi N,
    16. El Jaoudi R,
    17. Benrahma H,
    18. Elattar J,
    19. Mentag R,
    20. Sbabou L,
    21. Nejjari C,
    22. Amzazi S,
    23. Belyamani L,
    24. Ibrahimi A
    . 2020. Genomic diversity and hotspot mutations in 30,983 SARS-CoV-2 genomes: moving toward a universal vaccine for the “confined virus”? bioRxiv https://www.biorxiv.org/content/10.1101/2020.06.20.163188v1.
  9. 9.↵
    1. Laha S,
    2. Chakraborty J,
    3. Das S,
    4. Manna SK,
    5. Biswas S,
    6. Chatterjee R
    . 2020. Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission. Infect Genet Evol 85:104445. doi:10.1016/j.meegid.2020.104445.
    OpenUrlCrossRef
  10. 10.↵
    1. Patro LPP,
    2. Sathyaseelan C,
    3. Uttamrao PP,
    4. Rathinavelan T
    . 2020. Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates. bioRxiv https://www.biorxiv.org/content/10.1101/2020.07.31.230987v3.
  11. 11.↵
    1. Singer J,
    2. Gifford R,
    3. Cotten M,
    4. Robertson D
    . 2020. CoV-GLUE: a Web application for tracking SARS-CoV-2 genomic variation. Preprints doi:10.20944/preprints202006.0225.v1.
    OpenUrlCrossRef
  12. 12.↵
    1. Elbe S,
    2. Buckland-Merrett G
    . 2017. Data, disease and diplomacy: GISAID's innovative contribution to global health. Glob Chall 1:33–46. doi:10.1002/gch2.1018.
    OpenUrlCrossRefPubMed
  13. 13.↵
    1. Shu Y,
    2. McCauley J
    . 2017. GISAID: global initiative on sharing all influenza data - from vision to reality. Euro Surveill 22:30494. https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2017.22.13.30494.
    OpenUrlCrossRefPubMed
  14. 14.↵
    1. Aiewsakun P,
    2. Wongtrakoongate P,
    3. Thawornwattana Y,
    4. Hongeng S,
    5. Thitithanyanont A
    . 2020. SARS-CoV-2 genetic variations associated with COVID-19 severity. medRxiv https://www.medrxiv.org/content/10.1101/2020.05.27.20114546v1.
  15. 15.↵
    1. Toyoshima Y,
    2. Nemoto K,
    3. Matsumoto S,
    4. Nakamura Y,
    5. Kiyotani K
    . 2020. SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. J Hum Genet 65:1075–1082. doi:10.1038/s10038-020-0808-9.
    OpenUrlCrossRefPubMed
  16. 16.↵
    1. Zhang X,
    2. Tan Y,
    3. Ling Y,
    4. Lu G,
    5. Liu F,
    6. Yi Z,
    7. Jia X,
    8. Wu M,
    9. Shi B,
    10. Xu S,
    11. Chen J,
    12. Wang W,
    13. Chen B,
    14. Jiang L,
    15. Yu S,
    16. Lu J,
    17. Wang J,
    18. Xu M,
    19. Yuan Z,
    20. Zhang Q,
    21. Zhang X,
    22. Zhao G,
    23. Wang S,
    24. Chen S,
    25. Lu H
    . 2020. Viral and host factors related to the clinical outcome of COVID-19. Nature 583:437–440. doi:10.1038/s41586-020-2355-0.
    OpenUrlCrossRefPubMed
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Mutation Profile of SARS-CoV-2 Genome Sequences Originating from Eight Israeli Patient Isolates
Galia Zaide, Inbar Cohen-Gihon, Ofir Israeli, Dana Stein, Ohad Shifman, Shay Weiss, Irit Simon, Orly Laskar, Adi Beth-Din, Anat Zvi
Microbiology Resource Announcements Jan 2021, 10 (1) e01387-20; DOI: 10.1128/MRA.01387-20

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print
Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Microbiology Resource Announcements article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Mutation Profile of SARS-CoV-2 Genome Sequences Originating from Eight Israeli Patient Isolates
(Your Name) has forwarded a page to you from Microbiology Resource Announcements
(Your Name) thought you would be interested in this article in Microbiology Resource Announcements.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Mutation Profile of SARS-CoV-2 Genome Sequences Originating from Eight Israeli Patient Isolates
Galia Zaide, Inbar Cohen-Gihon, Ofir Israeli, Dana Stein, Ohad Shifman, Shay Weiss, Irit Simon, Orly Laskar, Adi Beth-Din, Anat Zvi
Microbiology Resource Announcements Jan 2021, 10 (1) e01387-20; DOI: 10.1128/MRA.01387-20
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • ANNOUNCEMENT
    • ACKNOWLEDGMENT
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About MRA
  • Editor in Chief
  • Board of Editors
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • Getting Started
  • Submit a Manuscript
  • Author Warranty
  • Ethics
  • Contact Us
  • ASM Author Center

Follow #MRAJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X