Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders

Brazils COVID-19 response has faced challenges due to the continuous emergence of variants of concern (VOCs), emphasizing the need for ongoing genomic surveillance and retrospective analyses of past epidemic waves. Rio Grande do Sul (RS), Brazils southernmost state, has crucial international borders and trades with Argentina and Uruguay, along with significant domestic connections. The source and sink of transmission with both national and international hubs raises questions about the RS role in the transmission of the virus, which has not been fully explored. Nasopharyngeal samples from various municipalities in RS were collected between June 2020 and July 2022. SARS-CoV-2 whole genome amplification and sequencing were performed using high-throughput Illumina sequencing. Bioinformatics analysis encompassed the development of scripts and tools to take into account epidemiological information to reduce sequencing disparities bias among the regions/countries, genome assembly, and large-scale phylogenetic reconstruction. Here, we sequenced 1,480 SARS-CoV-2 genomes from RS, covering all major regions. Sequences predominantly represented Gamma (April-June 2021) and Omicron (January-July 2022) variants. Phylogenetic analysis revealed a regional pattern for transmission dynamics, particularly with Southeast Brazil for Gamma, and a range of inter-regional connections for Delta and Omicron within the country. On the other hand, international and cross-border transmission with Argentina and Uruguay was rather limited. We evaluated the three VOCs circulation over two years in RS using a new subsampling strategy based on the number of cases in each state during the circulation of each VOC. In summary, the retrospective analysis of genomic surveillance data demonstrated that virus transmission was less intense between country borders than within the country. These findings suggest that while non-pharmacological interventions were effective to mitigate transmission across international land borders in RS, they were unsuficient to contain transmission at the domestic level.