Integration of Syndromic Surveillance and Rapid Genomic Response Enables Early Detection of Emerging SARS-CoV-2 Variants in Rio de Janeiro, Brazil

The history of recent epidemics or pandemics makes clear that delays in generating and releasing genomic data can directly limit our ability to detect, understand, and respond to emerging threats. Influenza-like illness (ILI) sentinel surveillance remains central to respiratory virus monitoring. Between September 2024 and July 2025, during episodic increases in ILI cases, in Rio de Janeiro, Brazil, an enhanced genomic surveillance strategy was implemented through collaboration between the Municipal Health Secretariat and the Laboratory of Respiratory Viruses and Measles (LVRE/IOC/Fiocruz). The strategy was triggered by epidemiological alerts from primary healthcare units performing routine SARS-CoV-2 antigen-detection rapid tests (Ag-RDTs). Increases in positivity prompted second-line RT-PCR and genomic sequencing. More than 200 nasopharyngeal samples were collected across 2-3 epidemiological weeks during each surge. SARS-CoV-2 RT-PCR–confirmed positives and samples with Ct