Genetic Analysis of SARS-CoV-2 in Armenia

Description of the Study:

• Title: Genetic analysis of SARS-CoV-2 in Armenia.
• Principal Investigator: Arsen Arakelyan.
• Co-investigators: Diana Avetyan, Siras Hakobyan,Maria Nikoghosyan, Roksana Zakharyan, Tamara Sirunyan, Gisane Khachatryan, Nelly Muradyan and Andranik Chavushyan.
• Centres of Implementation: Institute of Molecular Biology NAS RA, Department of Bioengineering and Bioinformatics of the Russian-Armenian University.
• Study Population: 24 Clinical samples from COVID-19 positive patients.
• Study Type: Experimental research.
• Methods: Nanopore sequencing, variant calling, functional annotation, phylogenetic analysis.

Objectives of the Study:

Principal Objective: Genetic characterization of clinical isolates of SARS-COV-2 in Armenia using whole-genome nanopore sequencing. This study can contribute to public health actions by providing phylogenetic structure of disease outbreak, trace transmission networks, identify new mutations in the viral genome associated with changes in transmission rates, disease course, and interfering with diagnostic tests.

More about this Study:

Scientific Context: Almost a year has passed since the official registration of the first case of coronavirus infection in the Republic of Armenia. However, until now, it has not been determined which particular mutations of the SARS-CoV-2 are common in Armenia. On the other hand, understanding the type of mutation is very important from an epidemiological point of view.

Based on the above, the present study was designed within the framework of collaboration between the Human Genome and Immunomics Laboratory of the Institute of Molecular Biology of the Armenian National Academy of Sciences, the Bionformatics Group and the researchers of the Department of Bioengineering, Bioinformatics and Molecular Biology of the Russian-Armenian University.

As a result of this collaboration, third-generation sequencing was made possible. Work on the identification of virus variants and analysis of mutations in the genome is still in progress. According to preliminary data, all the samples contain the D614G mutation in the S gene (Spike glycoprotein) that ensures the interaction of the virus with human cells. This variant of the virus was identified in February 2020 and is very common throughout the world.

The 12 samples studied in this study did not contain the South – African and British variants of the coronavirus.

The samples were obtained from the “Reference” Laboratory of the « Center for Epidemic Control and Prevention » of the Ministry of Health of Armenia. The results will be submitted to the Center for epidemiological purposes.

Acknowlegments: The third-generation sequencer and all the necessary accompanying equipment were obtained through the implementation of the Innovation Grants Fund program at the Armenian-Russian University of Armenia and grants provided by the equipment manufacturer “Seeding Labs” in 2017 and 2019. Some of the necessary reagents were provided by Lilit Nersisyan, PhD, postdoc at Karolinska University in Switzerland, and another part was purchased thanks to funding from the Armenian-Russian University. Bioinformatics analysis was performed by the resources of the Institute of Informatics and Automatization Problems of the National Academy of Sciences.