Viral genotype and the pace of epidemic waves: an assessment from SARS-CoV 2 genomics and wastewater surveillance data.

The SARS-CoV-2 pandemic was characterized by multiple epidemic waves, whose geographical non-synchronicity remains not fully understood. This study aimed to characterize this phenomenon at local and regional scales. To this end, we compared SARS-CoV-2 epidemics in a geographically isolated city (Trelew, Chubut, Argentina) with country-wide data between April 2020 and February 2022. This period encompassed distinct phases defined by non-pharmacological interventions, changes in population immunity, and shifts in dominant viral lineages. Routine daily case reports and clinical genomics data were integrated with local wastewater data collected weekly. Three epidemic waves were identified: the first hit the study site three months after the national peak, the second with a one-month delay, and the third virtually without delay. Wastewater samples analyzed for SARS-CoV-2 RNA by RT-qPCR were used in cross-correlation analyses to assess temporal relationships among datasets. These analyses confirmed a progressive reduction in epidemic asynchronicity, independent of testing or reporting practices. The gradual reduction in the delay was matched with the emergence of viral lineages with progressively higher transmissibility. The first wave was dominated by lineage B.1.499, endemic in Argentina; the second by the co-circulation of Alpha, Gamma, and Lambda variants typical of South America; and the third by the Delta and Omicron variants. These findings highlight the influence of viral evolution on the temporal synchronization of epidemic waves underscoring the relevance of integrated genomic and environmental surveillance.