Host Genetic Variants Potentially Associated With SARS-CoV-2: A Multi-Population Analysis
<h3>Background</h3><p dir="ltr">Clinical outcomes of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) showed enormous inter-individual and inter-population differences, possibly due to host genetics difference...
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2020
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| _version_ | 1864513512323153920 |
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| author | Maria K. Smatti (4675852) |
| author2 | Yasser A. Al-Sarraj (9452585) Omar Albagha (8977856) Hadi M. Yassine (4675846) |
| author2_role | author author author |
| author_facet | Maria K. Smatti (4675852) Yasser A. Al-Sarraj (9452585) Omar Albagha (8977856) Hadi M. Yassine (4675846) |
| author_role | author |
| dc.creator.none.fl_str_mv | Maria K. Smatti (4675852) Yasser A. Al-Sarraj (9452585) Omar Albagha (8977856) Hadi M. Yassine (4675846) |
| dc.date.none.fl_str_mv | 2020-10-02T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.3389/fgene.2020.578523 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Host_Genetic_Variants_Potentially_Associated_With_SARS-CoV-2_A_Multi-Population_Analysis/26095087 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Genetics Biomedical and clinical sciences Clinical sciences Immunology COVID-19 SARS-CoV-2 host genetics susceptibility SNPs |
| dc.title.none.fl_str_mv | Host Genetic Variants Potentially Associated With SARS-CoV-2: A Multi-Population Analysis |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <h3>Background</h3><p dir="ltr">Clinical outcomes of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) showed enormous inter-individual and inter-population differences, possibly due to host genetics differences. Earlier studies identified single nucleotide polymorphisms (SNPs) associated with SARS-CoV-1 in Eastern Asian (EAS) populations. In this report, we aimed at exploring the frequency of a set of genetic polymorphisms that could affect SARS-CoV-2 susceptibility or severity, including those that were previously associated with SARS-CoV-1.</p><h3>Methods</h3><p dir="ltr">We extracted the list of SNPs that could potentially modulate SARS-CoV-2 from the genome wide association studies (GWAS) on SARS-CoV-1 and other viruses. We also collected the expression data of these SNPs from the expression quantitative trait loci (eQTLs) databases. Sequences from Qatar Genome Programme (QGP, n = 6,054) and 1000Genome project were used to calculate and compare allelic frequencies (AF).</p><h3>Results</h3><p dir="ltr">A total of 74 SNPs, located in 10 genes: ICAM3, IFN-γ, CCL2, CCL5, AHSG, MBL, Furin, TMPRSS2, IL4, and CD209 promoter, were identified. Analysis of Qatari genomes revealed significantly lower AF of risk variants linked to SARS-CoV-1 severity (CCL2, MBL, CCL5, AHSG, and IL4) compared to that of 1000Genome and/or the EAS population (up to 25-fold change). Conversely, SNPs in TMPRSS2, IFN-γ, ICAM3, and Furin were more common among Qataris (average 2-fold change). Inter-population analysis showed that the distribution of risk alleles among Europeans differs substantially from Africans and EASs. Remarkably, Africans seem to carry extremely lower frequencies of SARS-CoV-1 susceptibility alleles, reaching to 32-fold decrease compared to other populations.</p><h3>Conclusion</h3><p dir="ltr">Multiple genetic variants, which could potentially modulate SARS-CoV-2 infection, are significantly variable between populations, with the lowest frequency observed among Africans. Our results highlight the importance of exploring population genetics to understand and predict COVID-19 outcomes. Indeed, further studies are needed to validate these findings as well as to identify new genetic determinants linked to SARS-CoV-2</p><h2>Other Information</h2><p dir="ltr">Published in: Frontiers in Genetics<br>License: <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.3389/fgene.2020.578523" target="_blank">https://dx.doi.org/10.3389/fgene.2020.578523</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_40299fc0242151489eb3d6c2803e6f1b |
| identifier_str_mv | 10.3389/fgene.2020.578523 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/26095087 |
| publishDate | 2020 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Host Genetic Variants Potentially Associated With SARS-CoV-2: A Multi-Population AnalysisMaria K. Smatti (4675852)Yasser A. Al-Sarraj (9452585)Omar Albagha (8977856)Hadi M. Yassine (4675846)Biological sciencesGeneticsBiomedical and clinical sciencesClinical sciencesImmunologyCOVID-19SARS-CoV-2host geneticssusceptibilitySNPs<h3>Background</h3><p dir="ltr">Clinical outcomes of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) showed enormous inter-individual and inter-population differences, possibly due to host genetics differences. Earlier studies identified single nucleotide polymorphisms (SNPs) associated with SARS-CoV-1 in Eastern Asian (EAS) populations. In this report, we aimed at exploring the frequency of a set of genetic polymorphisms that could affect SARS-CoV-2 susceptibility or severity, including those that were previously associated with SARS-CoV-1.</p><h3>Methods</h3><p dir="ltr">We extracted the list of SNPs that could potentially modulate SARS-CoV-2 from the genome wide association studies (GWAS) on SARS-CoV-1 and other viruses. We also collected the expression data of these SNPs from the expression quantitative trait loci (eQTLs) databases. Sequences from Qatar Genome Programme (QGP, n = 6,054) and 1000Genome project were used to calculate and compare allelic frequencies (AF).</p><h3>Results</h3><p dir="ltr">A total of 74 SNPs, located in 10 genes: ICAM3, IFN-γ, CCL2, CCL5, AHSG, MBL, Furin, TMPRSS2, IL4, and CD209 promoter, were identified. Analysis of Qatari genomes revealed significantly lower AF of risk variants linked to SARS-CoV-1 severity (CCL2, MBL, CCL5, AHSG, and IL4) compared to that of 1000Genome and/or the EAS population (up to 25-fold change). Conversely, SNPs in TMPRSS2, IFN-γ, ICAM3, and Furin were more common among Qataris (average 2-fold change). Inter-population analysis showed that the distribution of risk alleles among Europeans differs substantially from Africans and EASs. Remarkably, Africans seem to carry extremely lower frequencies of SARS-CoV-1 susceptibility alleles, reaching to 32-fold decrease compared to other populations.</p><h3>Conclusion</h3><p dir="ltr">Multiple genetic variants, which could potentially modulate SARS-CoV-2 infection, are significantly variable between populations, with the lowest frequency observed among Africans. Our results highlight the importance of exploring population genetics to understand and predict COVID-19 outcomes. Indeed, further studies are needed to validate these findings as well as to identify new genetic determinants linked to SARS-CoV-2</p><h2>Other Information</h2><p dir="ltr">Published in: Frontiers in Genetics<br>License: <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.3389/fgene.2020.578523" target="_blank">https://dx.doi.org/10.3389/fgene.2020.578523</a></p>2020-10-02T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.3389/fgene.2020.578523https://figshare.com/articles/journal_contribution/Host_Genetic_Variants_Potentially_Associated_With_SARS-CoV-2_A_Multi-Population_Analysis/26095087CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/260950872020-10-02T03:00:00Z |
| spellingShingle | Host Genetic Variants Potentially Associated With SARS-CoV-2: A Multi-Population Analysis Maria K. Smatti (4675852) Biological sciences Genetics Biomedical and clinical sciences Clinical sciences Immunology COVID-19 SARS-CoV-2 host genetics susceptibility SNPs |
| status_str | publishedVersion |
| title | Host Genetic Variants Potentially Associated With SARS-CoV-2: A Multi-Population Analysis |
| title_full | Host Genetic Variants Potentially Associated With SARS-CoV-2: A Multi-Population Analysis |
| title_fullStr | Host Genetic Variants Potentially Associated With SARS-CoV-2: A Multi-Population Analysis |
| title_full_unstemmed | Host Genetic Variants Potentially Associated With SARS-CoV-2: A Multi-Population Analysis |
| title_short | Host Genetic Variants Potentially Associated With SARS-CoV-2: A Multi-Population Analysis |
| title_sort | Host Genetic Variants Potentially Associated With SARS-CoV-2: A Multi-Population Analysis |
| topic | Biological sciences Genetics Biomedical and clinical sciences Clinical sciences Immunology COVID-19 SARS-CoV-2 host genetics susceptibility SNPs |