Molecular Analysis of SARS-CoV-2 Lineages in Armenia

Viruses. 2022 May 17;14(5):1074. doi: 10.3390/v14051074.


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.

Keywords: Armenia; COVID-19; Illumina sequencing; SARS-CoV-2; coronavirus; nanopore sequencing; whole-genome sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Armenia / epidemiology
  • COVID-19* / epidemiology
  • High-Throughput Nucleotide Sequencing
  • Humans
  • SARS-CoV-2* / genetics

Supplementary concepts

  • SARS-CoV-2 variants

Grants and funding

This research was funded by SeedingLabs “Instrumental Access” -2017 (A.A.) and -2019 (R.Z.), as well as the Educational-Scientific Center of Excellence for “Genetic engineering, genome editing and 3rd generation sequencing” grant in the frames of the “Competitive Innovation Fund” under “Education Improvement” project supported by World Bank (2019–2021, A.A. and R.Z.), Armenian National Science and Education Fund (NS-molbio-2522 to A.A.) the State Target Program of the Government of the Republic of Armenia under grant agreement № 1-8/20TB project “Creating a Cloud Computing Environment for Solving Scientific and Applied Problems”.