Molecular Analysis of SARS-CoV-2 Lineages in Armenia

Viruses

Lilit Nersisyan¹  Siras Hakobyan²  Shah A. Mohamed Bakhash³  Keith R. Jerome³  Alexander L. Greninger³  Pavitra Roychoudhury³  Maria Nikoghosyan⁴  Anahit Hovhannisyan⁴  Andranik Chavushyan⁵  Nelli Muradyan⁵  Lilit Ghukasyan⁵  Gisane Khachatryan⁵  Roksana Zakharyan⁵  Varduhi Hayrapetyan⁵  Arsen Arakelyan⁵  Tamara Sirunyan⁵  Diana Avetyan⁵  Mher Davidyants⁶  Lyudmila Niazyan⁶  Gayane Melik-Andreasyan⁷  Shushan Sargsyan⁷ 

[1] Armenian Bioinformatics Institute, Yerevan 0014, Armenia;Bioinformatics Group, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia;Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98102, USA;Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia;Laboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia;NORK Infection Clinical Hospital, MoH RA, Yerevan 0047, Armenia;National Center of Disease Control and Prevention, Ministry of Health RA, Yerevan 0025, Armenia;

关键词: COVID-19;    SARS-CoV-2;    coronavirus;    nanopore sequencing;    Illumina sequencing;    whole-genome sequencing;   

DOI  :  10.3390/v14051074

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown