Genotypic diversity of SARS-CoV-2 during the pandemic and early post-pandemic period: Summary of the PhD thesis in Medical Sciences: 313.02 –Medical Microbiology and Virology

Abstract

Relevance. SARS-CoV-2 infection remains a major public health challenge because of the continuing evolution of the virus and the emergence of genetic variants that affect transmission and disease control. Genomic monitoring is essential for epidemiological surveillance and for identifying circulating variants. Aim of the study. To identify SARS-CoV-2 variants circulating in the Republic of Moldova and to perform phylogenetic analysis of the detected isolates, with the aim of improving COVID19 surveillance and morbidity control measures. Objectives of the study. To provide a phylogenetic characterization of SARS-CoV-2 isolates detected in the Republic of Moldova; to study SARS-CoV-2 evolution by identifying substitutions, insertions, and deletions and comparing them with global viral genome diversity; to analyze SARS-CoV-2 circulation dynamics and the emergence of new genetic variants, including the relationship between viral genotypes and epidemiological data; to assess wastewater monitoring as a method for predicting epidemiological trends in SARS-CoV-2 infection; and to evaluate the impact of different SARS-CoV-2 genotypes in order to support proposals for improving the laboratory diagnosis of COVID-19. Scientific novelty and originality. Original data on the genotypic and phenotypic characteristics of SARS-CoV-2 circulating in the Republic of Moldova were obtained for the first time using modern genomic sequencing and bioinformatic analysis. The study identified SARSCoV-2 genovariants in clinical and wastewater samples, assessed their position within global phylogenetic trees, and analyzed the molecular evolution of the virus. The findings contributed to forecasting epidemic dynamics and optimizing surveillance and control measures for COVID-19. The obtained study results. The research determined the genetic structure and distribution of SARS-CoV-2 lineages in the Republic of Moldova during 2021–2025. Dominant mutations were identified, and their impact on the biological properties of the virus was assessed. The study also demonstrated the value of wastewater monitoring for early detection of circulating variants, evaluated the performance of bioinformatic tools used for sequencing-data analysis, and developed proposals for improving laboratory diagnosis and epidemiological surveillance. Theoretical background. The study deepens current understanding of the molecular evolution of SARS-CoV-2 and the mechanisms of viral adaptation, providing a scientific basis for the development of modern genomic surveillance and epidemiological management strategies. The research practical value. The findings were applied through the development of goodpractice guidelines in genomic sequencing, the update of the national clinical protocol, and the integration of the data into the training of students, resident physicians, and specialists in the field. Implementation of scientific results. The research findings were implemented through the development of a guide on metagenomic sequencing, preparation of a monograph on nucleic acid sequencing, update of the National Clinical Protocol on COVID-19, and use of the results in healthcare institutions, epidemiological surveillance, and university education. PhD thesis structure. The thesis includes an introduction, four chapters, general conclusions and recommendations, a bibliography of 189 references, 12 annexes, 94 pages of main text, 8 tables, and 42 figures. The results have been published in 32 scientific papers. Keywords: COVID-19; SARS-CoV-2; sequencing; NGS; viral genome; genetic monitoring; mutation variants; wastewater.