Genome Similarities between Human-Derived and Mink-Derived SARS-CoV-2 Make Mink a Potential Reservoir of the Virus
Abstract
:1. Introduction
2. Methods
2.1. Mink-Derived SARS-CoV-2 Genome Sequences
2.2. Mutational Analysis of the Mink-Derived SARS-CoV-2 Genome Sequences
3. Results
3.1. Pipeline for the Mutation Analysis
3.2. SARS-CoV-2 Hosts Range
3.3. The Phylogenetic Tree of SARS-CoV-2 Genomes Derived from Various Hosts
3.4. The Mutations in SARS-CoV-2 Genome Derived from the Netherlands and Denmark Mink Farms
3.5. The ΔH69/V70 and Several Other Mutations Were Prevalent in Mink-Derived SARS-CoV-2 Genome
3.6. Mutations at Amino Acid Level
3.7. The Frame-Shift and Nonsense Mutations
4. Discussions
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
GISAID | Global initiative on sharing all influenza data |
NCBI | National Center for Biotechnology Information |
NSP6 | Non-structural protein 6 |
ORF-8 | Open Reading Frame-8 |
UTRs | Untranslated regions |
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S. No. | Name | Sequences |
---|---|---|
1 | Human (Homo sapiens) | 3,240,911 |
2 | Mink (Neovison vison) | 994 |
3 | Cat (Felis catus) | 70 |
4 | Lion (Panthera leo) | 37 |
5 | Dog (Canis lupus familiaries | 28 |
6 | Pangolin (Manis javanica) | 19 |
7 | Tiger (Panthera tigris jacksoni) | 13 |
8 | Otter (Aonyx cinereus) | 5 |
9 | Mouse (Mus musculus) | 4 |
10 | Bat (Rhinolophus malayanus) | 4 |
11 | Bat (Rhinolophus shameli) | 2 |
12 | Bat (Rhinolophus affinis) | 1 |
13 | Monkey (Chlorocebus sabaeus) | 1 |
14 | Pangolin (Manis pentadactyla) | 1 |
S. No. | Mutation | Amino Acid | ORFs | Denmark % | Netherlands % |
---|---|---|---|---|---|
1 | C241T | N/A | 5′-UTR | 100.0 | 90.7 |
2 | TTA516--- | M84 deletion | 1a | 83.5 | 0.0 |
3 | C1380T | A372V | 1a | 0.0 | 50.9 |
4 | T3037C | Silent | 1a | 100.0 | 77.6 |
5 | C5144T | Silent | 1a | 84.2 | 0.0 |
6 | ATA6510--- | S2082 deletion | 1a | 84.2 | 16.0 |
7 | C11776T | Silent | 1a | 84.2 | 0.0 |
8 | G14274A | Silent | 1b | 0.0 | 51.4 |
9 | C14408T | P314L | 1b | 100.0 | 89.3 |
10 | C15656T | T730I | 1b | 93.2 | 5.7 |
11 | ACATGT21766------ | H69/V70 deletion | S | 84.2 | 0.0 |
12 | A22920T | Y453F | S | 90.2 | 19.8 |
13 | A23403G | D614G | S | 100.0 | 89.3 |
14 | A24862G | Silent | S | 0.0 | 51.4 |
15 | C25936T | H182Y | 3a | 93.2 | 43.9 |
16 | G28854T | S194L | N | 84.2 | 0.0 |
17 | GGG28881AAC | RG203KR | N | 97.7 | 0.0 |
18 | T29726- | - | 10/3′-UTR | 83.5 | 0.0 |
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Khalid, M.; Alshishani, A.; Al-ebini, Y. Genome Similarities between Human-Derived and Mink-Derived SARS-CoV-2 Make Mink a Potential Reservoir of the Virus. Vaccines 2022, 10, 1352. https://doi.org/10.3390/vaccines10081352
Khalid M, Alshishani A, Al-ebini Y. Genome Similarities between Human-Derived and Mink-Derived SARS-CoV-2 Make Mink a Potential Reservoir of the Virus. Vaccines. 2022; 10(8):1352. https://doi.org/10.3390/vaccines10081352
Chicago/Turabian StyleKhalid, Mohammad, Anas Alshishani, and Yousef Al-ebini. 2022. "Genome Similarities between Human-Derived and Mink-Derived SARS-CoV-2 Make Mink a Potential Reservoir of the Virus" Vaccines 10, no. 8: 1352. https://doi.org/10.3390/vaccines10081352
APA StyleKhalid, M., Alshishani, A., & Al-ebini, Y. (2022). Genome Similarities between Human-Derived and Mink-Derived SARS-CoV-2 Make Mink a Potential Reservoir of the Virus. Vaccines, 10(8), 1352. https://doi.org/10.3390/vaccines10081352