Seasonal trends and molecular evolution of SARS-CoV-2 in acute respiratory illness patients during the fifth year of COVID-19, Thailand

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is relentlessly evolving, with emerging variants exhibiting heightened transmissibility and immune escape capabilities. Understanding the genetic diversity and seasonal transmission dynamics of SARS-CoV-2 in Thailand is crucial for implementing effective public health interventions. This study aims to elucidate the genetic diversity and seasonal transmission patterns of SARS-CoV-2 among patients with acute respiratory illness in Thailand in 2024. Among 8,096 Acute Respiratory Infection (ARI) cases analyzed, 1,152 samples tested positive for SARS-CoV-2, resulting in a positivity rate of 14.2%. The majority of infections occurred during a significant Outbreak from late summer to early rainy season, particularly between April and June, accounting for nearly 49% of all positive cases. The highest infection rate occurred in adults aged 31-40 years, with no significant association between gender and infection status (p = 0.583). Extensive genomic sequencing identified over seven distinct SARS-CoV-2 lineages, with the JN.1 lineage dominating early in the year. Recombinant variants, notably XEC, XDV.1, and XDY, emerged as significant contributors to the evolving landscape, reaching a prevalence of 57.1% by December. Phylogenetic analyses demonstrated a consistent evolutionary rate and identified critical emergence dates for new lineages, underscoring the virus's ongoing evolution in Thailand. Our findings emphasize the necessity of continuous genomic surveillance for tracking variant transmission dynamics and managing public health responses effectively. Furthermore, the evolving genetic landscape of SARS-CoV-2 highlights the urgent need for adaptive vaccination strategies aligned with seasonal transmission patterns in Thailand.