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SARS-CoV-2 lineages and Variants Of Concern in patients from a university hospital in Tirana,  Albania, January-February 2021

A Spitaleri(1) F Saluzzo(1) S Battaglia(1) V Poletti de Chaurand(1,2) A M Cabibbe(1) S Bino(4) S Bala(5) H Hafizi(5) P Kapisyzi(5) L Suraj(3) A Vasili(4) D M Cirillo(1) S Tafaj(3)

1:Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.; 2:Dipartimento di Medicina e chirurgia, Università degli studi di Milano Bicocca, Milan, Italy.; 3:Microbiology Department National TB Reference Laboratory, University Hospital "Shefqet Ndroqi", Tirana, Albania.; 4: Control of Infectious Diseases Department, Institute of Public Health,Tirana, Albania.; 5:Pneumology Service, University Hospital "Shefqet Ndroqi", Tirana, Albania.

The emergence of SARS-CoV-2 Variants Of Concern (VOC) has boosted the attention to the molecular characterization of the virus. Sequencing and data sharing proved essential for tracing the origin and spreading of the virus mutations over time. 

From the first week of January to the first week of March 2021, Albania reported 53087 confirmed cases and 728 deaths due to COVID-19. For this study we randomly selected 122 nasopharyngeal specimens (NPS) among the patients SARS-CoV-2 positive hospitalized at University Hospital Shefqet Ndroqi (UHSN).

The aim of this study was to analyze the SARS-CoV-2 viral genomes from strains collected in Albania at the beginning of 2021, when the Alpha variant became a worldwide major public health concern. We compared performances and results of Illumina and Nanopore sequencing techniques using ARTIC protocol V3, performing analysis over different common investigative tasks. Finally, we provided an overview of the virus transmission in Albania.

Our results show a good agreement match between the two sequencing technologies, allowing to properly characterize the SARS-CoV-2 clades. In particular, both sequencing defined the alpha variant VOC N501Y, D614G and P681H on S-spike, have similar trend as function of Ct values and the tanglegram comparison have an entanglement of 0.17, demonstrating a perfect phylogenesis analysis match.

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