Infection of urban rodents by SARS-CoV-2 in COVID-19 healthcare facilities in Brazzaville, Republic of the Congo

Abstract

BACKGROUND: Considering the global increase of COVID-19 cases in the healthcare facilities between 2020 and 2021, and the widespread presence of pest rodents in Brazzaville, we conducted this study at the end of the pandemic peak to assess the potential for urban rodents to be infected with SARS-CoV-2 in the Republic of the Congo. METHODS: Between April and December 2022, a total of 96 rodent were captured in three COVID-19 healthcare facilities in Brazzaville. Intestinal samples were tested for SARS-CoV-2 RNA using RT-qPCR, followed by nested RT-PCR targeting the RdRp gene and Sanger sequencing. Concurrently, serum samples were analysed to detect SARS-CoV-2 antibodies using the Luminex technology. RESULTS: SARS-CoV-2 RNA was detected in intestinal samples from nine (9.4%) rodent: 7/80 (8.7%) R. rattus, 1/13 (7.7%) R. tanezumi, and 1/2 (50%) M. musculus. Phylogenetic analyses using Nextclade and maximum likelihood phylogeny methods revealed substantial diversity among SARS-CoV-2 partial genome belonging to clades 20B, 20G, Recombinant, 21 K and 22B. Additionally, 9/96 (9.4%) rodents tested seropositive for SARS-CoV-2 antibodies. CONCLUSIONS: These findings provide evidence for the establishment of new SARS-CoV-2 reservoirs in certain animal populations, emphasizing the urgent need for continuous surveillance to prevent future outbreaks from animal sources.