Molecular Analysis of SARS-CoV-2 Lineages in Armenia
The sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina sequencing to describe the circulation of the virus lineages in Armenia. The analysis of 1...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-05-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/5/1074 |
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| author | Diana Avetyan Siras Hakobyan Maria Nikoghosyan Lilit Ghukasyan Gisane Khachatryan Tamara Sirunyan Nelli Muradyan Roksana Zakharyan Andranik Chavushyan Varduhi Hayrapetyan Anahit Hovhannisyan Shah A. Mohamed Bakhash Keith R. Jerome Pavitra Roychoudhury Alexander L. Greninger Lyudmila Niazyan Mher Davidyants Gayane Melik-Andreasyan Shushan Sargsyan Lilit Nersisyan Arsen Arakelyan |
| author_facet | Diana Avetyan Siras Hakobyan Maria Nikoghosyan Lilit Ghukasyan Gisane Khachatryan Tamara Sirunyan Nelli Muradyan Roksana Zakharyan Andranik Chavushyan Varduhi Hayrapetyan Anahit Hovhannisyan Shah A. Mohamed Bakhash Keith R. Jerome Pavitra Roychoudhury Alexander L. Greninger Lyudmila Niazyan Mher Davidyants Gayane Melik-Andreasyan Shushan Sargsyan Lilit Nersisyan Arsen Arakelyan |
| author_sort | Diana Avetyan |
| collection | DOAJ |
| description | The sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina sequencing to describe the circulation of the virus lineages in Armenia. The analysis of 145 full genomes identified six clades (19A, 20A, 20B, 20I, 21J, and 21K) and considerable intra-clade PANGO lineage diversity. Phylodynamic and transmission analysis allowed to attribute specific clades as well as infer their importation routes. Thus, the first two waves of positive case increase were caused by the 20B clade, the third peak caused by the 20I (Alpha), while the last two peaks were caused by the 21J (Delta) and 21K (Omicron) variants. The functional analyses of mutations in sequences largely affected epitopes associated with protective HLA loci and did not cause the loss of the signal in PCR tests targeting ORF1ab and N genes as confirmed by RT-PCR. We also compared the performance of nanopore and Illumina short-read sequencing and showed the utility of nanopore sequencing as an efficient and affordable alternative for large-scale molecular epidemiology research. Thus, our paper describes new data on the genomic diversity of SARS-CoV-2 variants in Armenia in the global context of the virus molecular genomic surveillance. |
| first_indexed | 2024-03-10T01:36:51Z |
| format | Article |
| id | doaj.art-d11cc83a617c47748c96fcd328e066c4 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T01:36:51Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-d11cc83a617c47748c96fcd328e066c42023-11-23T13:32:53ZengMDPI AGViruses1999-49152022-05-01145107410.3390/v14051074Molecular Analysis of SARS-CoV-2 Lineages in ArmeniaDiana Avetyan0Siras Hakobyan1Maria Nikoghosyan2Lilit Ghukasyan3Gisane Khachatryan4Tamara Sirunyan5Nelli Muradyan6Roksana Zakharyan7Andranik Chavushyan8Varduhi Hayrapetyan9Anahit Hovhannisyan10Shah A. Mohamed Bakhash11Keith R. Jerome12Pavitra Roychoudhury13Alexander L. Greninger14Lyudmila Niazyan15Mher Davidyants16Gayane Melik-Andreasyan17Shushan Sargsyan18Lilit Nersisyan19Arsen Arakelyan20Laboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, ArmeniaBioinformatics Group, Institute of Molecular Biology NAS RA, Yerevan 0014, ArmeniaInstitute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, ArmeniaLaboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, ArmeniaLaboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, ArmeniaLaboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, ArmeniaLaboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, ArmeniaLaboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, ArmeniaLaboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, ArmeniaLaboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, ArmeniaInstitute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, ArmeniaDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98102, USADepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98102, USADepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98102, USADepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98102, USANORK Infection Clinical Hospital, MoH RA, Yerevan 0047, ArmeniaNORK Infection Clinical Hospital, MoH RA, Yerevan 0047, ArmeniaNational Center of Disease Control and Prevention, Ministry of Health RA, Yerevan 0025, ArmeniaNational Center of Disease Control and Prevention, Ministry of Health RA, Yerevan 0025, ArmeniaArmenian Bioinformatics Institute, Yerevan 0014, ArmeniaLaboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, ArmeniaThe sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina sequencing to describe the circulation of the virus lineages in Armenia. The analysis of 145 full genomes identified six clades (19A, 20A, 20B, 20I, 21J, and 21K) and considerable intra-clade PANGO lineage diversity. Phylodynamic and transmission analysis allowed to attribute specific clades as well as infer their importation routes. Thus, the first two waves of positive case increase were caused by the 20B clade, the third peak caused by the 20I (Alpha), while the last two peaks were caused by the 21J (Delta) and 21K (Omicron) variants. The functional analyses of mutations in sequences largely affected epitopes associated with protective HLA loci and did not cause the loss of the signal in PCR tests targeting ORF1ab and N genes as confirmed by RT-PCR. We also compared the performance of nanopore and Illumina short-read sequencing and showed the utility of nanopore sequencing as an efficient and affordable alternative for large-scale molecular epidemiology research. Thus, our paper describes new data on the genomic diversity of SARS-CoV-2 variants in Armenia in the global context of the virus molecular genomic surveillance.https://www.mdpi.com/1999-4915/14/5/1074COVID-19SARS-CoV-2coronavirusnanopore sequencingIllumina sequencingwhole-genome sequencing |
| spellingShingle | Diana Avetyan Siras Hakobyan Maria Nikoghosyan Lilit Ghukasyan Gisane Khachatryan Tamara Sirunyan Nelli Muradyan Roksana Zakharyan Andranik Chavushyan Varduhi Hayrapetyan Anahit Hovhannisyan Shah A. Mohamed Bakhash Keith R. Jerome Pavitra Roychoudhury Alexander L. Greninger Lyudmila Niazyan Mher Davidyants Gayane Melik-Andreasyan Shushan Sargsyan Lilit Nersisyan Arsen Arakelyan Molecular Analysis of SARS-CoV-2 Lineages in Armenia Viruses COVID-19 SARS-CoV-2 coronavirus nanopore sequencing Illumina sequencing whole-genome sequencing |
| title | Molecular Analysis of SARS-CoV-2 Lineages in Armenia |
| title_full | Molecular Analysis of SARS-CoV-2 Lineages in Armenia |
| title_fullStr | Molecular Analysis of SARS-CoV-2 Lineages in Armenia |
| title_full_unstemmed | Molecular Analysis of SARS-CoV-2 Lineages in Armenia |
| title_short | Molecular Analysis of SARS-CoV-2 Lineages in Armenia |
| title_sort | molecular analysis of sars cov 2 lineages in armenia |
| topic | COVID-19 SARS-CoV-2 coronavirus nanopore sequencing Illumina sequencing whole-genome sequencing |
| url | https://www.mdpi.com/1999-4915/14/5/1074 |
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