Tracking SARS-CoV-2: Molecular epidemiology and surveillance in Health Region VIII, Buenos Aires, Argentina (2020-2021).

Abstract

To describe the classical and molecular epidemiology of SARS-CoV-2 in Health Region VIII (HRVIII, Buenos Aires Province, Argentina), we analyzed 120421 respiratory samples from patients with acute respiratory infection during the first two pandemic years. Complete genome or partial spike gene sequences were obtained for phylogenetic analyses to investigate viral introductions, transmission dynamics, and genetic diversity. Substitution rates were estimated for predominant lineages. SARS-CoV-2 positivity was significantly higher in 2020 (37.4%) than in 2021 (31.9%, p<0.001). In 2020, positivity was higher among travelers (41.7%) than residents (36.4%), a trend that reversed in 2021 (33.4% vs. 28.0%), reflecting the region's socioeconomic and touristic characteristics. The first wave peaked at epidemiological week (EW) 37 of 2020 and was dominated by lineages B.1.1.33, N.3, and B.1.499. A resurgence in early 2021 involved lineage N.5 and emerging Alpha and Lambda variants. The second wave peaked at EW 20 and featured cocirculation of Gamma and Lambda, which were later displaced by Delta after EW 31. Estimated substitution rates ranged from 2.4×10-4 to 6.8×10-4substitutions/site/year across different clades. This study provides a detailed overview of SARS-CoV-2 circulation in HRVIII and underscores the importance of integrating genomic surveillance into public health systems to monitor emerging variants and support timely response strategies.