Genomic Sequencing and Analysis of Eight Camel-Derived Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Isolates in Saudi Arabia
Abstract
:1. Introduction
2. Results
2.1. Genome Organization
2.2. Phylogenetic Analysis
2.3. MERS-CoV B Cell Epitope Analysis
3. Discussion
4. Materials and Methods
4.1. Sample Collection
4.2. RNA Extraction
4.3. Sequence Preparation
4.4. RNA Quantification and cDNA Conversion
4.5. Library Preparation and Sequencing
4.6. Gap Filling and Sanger Sequencing
4.7. Phylogenetic Trees and Evolutionary Dynamics
4.8. Prediction of MERS-CoV B Cell Epitopes
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Organism Name | Accession Number | S Protein Identity (%) | S Gene Identity (%) |
---|---|---|---|
MERS-COV | MT226600 * | 99.85 | 82.06 |
MERS-COV | MT226601 * | 99.85 | 81.97 |
MERS-COV | MT226602 * | 99.85 | 82.9 |
MERS-COV | MT226603 * | 99.70 | 82.31 |
MERS-COV | MT226604 * | 100.00 | 100.00 |
MERS-COV | MT226605 * | 99.93 | 82.53 |
MERS-COV | MT226606 * | 99.85 | 83.37 |
MERS-COV | MT226607 * | 99.85 | 82.51 |
MERS-COV | KJ713297 | 99.78 | 82.46 |
MERS-COV | KY673149 | 99.63 | 82.36 |
MERS-COV | KF600612 | 99.78 | 82.16 |
MERS-COV | KF186564 | 99.78 | 83.00 |
MERS-COV | KF600652 | 99.78 | 82.31 |
MERS-COV | KF961222 | 99.78 | 82.71 |
MERS-COV | KF192507 | 99.70 | 83.74 |
2019-nCOV | EPI_ISL_416432 | 27.44 | 39.16 |
2019-nCOV | EPI_ISL_416522 | 27.44 | 40.43 |
2019-nCOV | NC_045512 | 27.44 | 40.46 |
2019-nCOV | MN988713.1 | 27.44 | 39.98 |
Batcoronavirus | KF636752.1 | 27.88 | 39.27 |
Batcoronavirus | GU190215.1 | 26.90 | 39.95 |
Batcoronavirus | DQ648857.1 | 26.99 | 39.42 |
Batcoronavirus | MK211374.1 | 26.94 | 39.27 |
Bat SARS coronavirus HKU3-12 | GQ153547.1 | 66.32 | 65.78 |
Bat SARS-like coronavirus | KY417145.1 | 27.32 | 39.51 |
SARS-like coronavirus | KT444582.1 | 27.01 | 39.98 |
SARS-like coronavirus | AY278489.2 | 26.87 | 39.83 |
SARS coronavirus | NC_004718.3 | 26.87 | 39.22 |
SARS coronavirus | DQ497008.1 | 26.94 | 39.88 |
SARS coronavirus | FJ882957.1 | 26.94 | 39.44 |
SARS coronavirus | FJ882962.1 | 26.94 | 39.88 |
Strain | Start | End | Peptide | Length | Score | 3D Structure |
---|---|---|---|---|---|---|
MERS-CoV | 523 | 566 | YSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQ | 44 | 0.898 | A |
702 | 743 | STYGPLQTPVGCVLGLVNSSLFVEDCKLPLGQSLCALPDTPS | 42 | 0.88 | B | |
485 | 518 | PHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLV | 34 | 0.848 | C | |
90 | 99 | GHATGTTPQK | 10 | 0.839 | D | |
618 | 628 | QNCTAVGVRQQ | 11 | 0.827 | E | |
18 | 32 | YVDVGPDSVKSACIE | 15 | 0.801 | F | |
2019-nCov | 1071 | 1147 | QEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS | 77 | 0.88 | - |
92 | 192 | FASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVNCTFEYVSFKNLREF | 67 | 0.788 | - | |
328 | 364 | RFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVAD | 37 | 0.767 | - | |
553 | 564 | TESNKKFLPFQQ | 12 | 0.721 | - | |
SARS-CoV | 684 | 702 | DSSIAYSNNTIAIPTNFSI | 19 | 0.712 | - |
315 | 355 | RFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVL | 41 | 0.692 | - | |
765 | 797 | AQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKR | 33 | 0.638 | - |
Organism Name | Host | Country | Accession Number |
---|---|---|---|
MERS-COV | Camelus dromedarius | Saudi Arabia | MT226600 * |
MERS-COV | Camelus dromedarius | Saudi Arabia | MT226601 * |
MERS-COV | Camelus dromedarius | Saudi Arabia | MT226602 * |
MERS-COV | Camelus dromedarius | Saudi Arabia | MT226603 * |
MERS-COV | Camelus dromedarius | Saudi Arabia | MT226604 * |
MERS-COV | Camelus dromedarius | Saudi Arabia | MT226605 * |
MERS-COV | Camelus dromedarius | Saudi Arabia | MT226606 * |
MERS-COV | Camelus dromedarius | Saudi Arabia | MT226607 * |
MERS-COV | Camelus dromedarius | Saudi Arabia | KJ713297 |
MERS-COV | Camelus dromedarius | Oman | KY673149 |
MERS-COV | Homo sapiens | Saudi Arabia | KF600612 |
MERS-COV | Homo sapiens | Saudi Arabia | KF186564 |
MERS-COV | Homo sapiens | Saudi Arabia | KF600652 |
MERS-COV | Homo sapiens | Qatar | KF961222 |
MERS-COV | Homo sapiens | United Arab Emirates | KF192507 |
2019-nCOV | Homo sapiens | Saudi Arabia | EPI_ISL_416432 |
2019-nCOV | Homo sapiens | Saudi Arabia | EPI_ISL_416522 |
2019-nCOV | Homo sapiens | China | NC_045512 |
2019-nCOV | Homo sapiens | USA | MN988713.1 |
Batcoronavirus | Hipposideros pratti | China | KF636752.1 |
Batcoronavirus | Rhinolophus blasii | China | GU190215.1 |
Batcoronavirus | Rhinolophus macrotis | China | DQ648857.1 |
Batcoronavirus | Rhinolophus sp. | China | MK211374.1 |
Bat SARS coronavirus HKU3-12 | Homo sapiens | China | GQ153547.1 |
Bat SARS-like coronavirus | Rhinilophus ferrumequinum | China | KY417145.1 |
SARS-like coronavirus | Rhinolophus sinicus | China | KT444582.1 |
SARS-like coronavirus | Homo sapiens | China | AY278489.2 |
SARS coronavirus | Homo sapiens | Canada | NC_004718.3 |
SARS coronavirus | Mus musculus | USA | DQ497008.1 |
SARS coronavirus | Mus musculus | USA | FJ882957.1 |
SARS coronavirus | Mus musculus | USA | FJ882962.1 |
Primer Name | Sequence |
---|---|
Gap1_F1 | CCTCGTTCTCTTGCAGAACTT |
Gap1_R1 | CCGGACGAAACCGTGTATT |
Gap1_F2 | CACTTCCCCTCGTTCTCTTG |
Gap1_R2 | ACCGTGTATTGTGACCGAGA |
Gap2_F1 | ACCAATTGGCTTATAGCTCTAGT |
Cap2_R1 | CCTTTAGGATCCGCCTCAAA |
Gap3_F1 | GGGATTACCCTAAGTGTGATAGAG |
Gap3_R1 | GTGCACTGACATTAGCAGTTG |
Gap4_F1 | CTGGGTTGTACCCAACCATT |
Gap4_R1 | CGTGCTGTAGGGTAGTAAATCG |
Gap5_F1 | TTTGCCAGGTTGTGATGG |
Gap5_R1 | ATACTCTCTGTACTCTGTAGCAT |
Gap6_F1 | TTCTTTACTTACCTGTGTAACCTCA |
Gap6_R1 | TCATAGGAGTGGAATTTCTCCAAA |
Gap7_F1 | CAGCATCAGCTCGTGATCTT |
Gap7_R1 | CTCCCAGAGCCTGATTAAACTTAT |
Gap8_F1 | CTCCTTTGGCCGTAGATGTT |
Gap8_R1 | CCGCTAGCAGGAATGTATGT |
Gap8_F2 | CCTTTGGCCGTAGATGTTGT |
Gap8_R2 | GCCGCTAGCAGGAATGTATG |
Gap9_F1 | AGATCGCGGCAATCGTT |
Gap9_R1 | GGCACTGTTCACTTGCAATC |
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Al-Shomrani, B.M.; Manee, M.M.; Alharbi, S.N.; Altammami, M.A.; Alshehri, M.A.; Nassar, M.S.; Bakhrebah, M.A.; Al-Fageeh, M.B. Genomic Sequencing and Analysis of Eight Camel-Derived Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Isolates in Saudi Arabia. Viruses 2020, 12, 611. https://doi.org/10.3390/v12060611
Al-Shomrani BM, Manee MM, Alharbi SN, Altammami MA, Alshehri MA, Nassar MS, Bakhrebah MA, Al-Fageeh MB. Genomic Sequencing and Analysis of Eight Camel-Derived Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Isolates in Saudi Arabia. Viruses. 2020; 12(6):611. https://doi.org/10.3390/v12060611
Chicago/Turabian StyleAl-Shomrani, Badr M., Manee M. Manee, Sultan N. Alharbi, Mussad A. Altammami, Manal A. Alshehri, Majed S. Nassar, Muhammed A. Bakhrebah, and Mohamed B. Al-Fageeh. 2020. "Genomic Sequencing and Analysis of Eight Camel-Derived Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Isolates in Saudi Arabia" Viruses 12, no. 6: 611. https://doi.org/10.3390/v12060611