Human rhinovirus and respiratory syncytial virus genotypes in Sudden Unexpected Death in Infancy (SUDI) cases at Tygerberg Hospital, Cape Town, South Africa

Abstract

Infant mortality remains a major global concern. Sudden unexpected death in infancy (SUDI) is reported globally and accounted for 40% of infant deaths between 2012 and 2016 in the Western Cape. Research highlighting molecular typing of respiratory viruses in SUDI cases is lacking. A total of 116 PCR-positive human rhinovirus (HRV) and respiratory syncytial virus (RSV) swab samples collected from the lungs and trachea of SUDI cases admitted to Tygerberg Medico-legal Mortuary between 2015 and 2019 were included and underwent automated nucleic acid extraction, one-step, nested RT-PCR, and amplification by gel electrophoresis before sequencing and phylogenetic analysis. The median age of the infants were 10.9 weeks. Three distinct HRV species were identified; HRV-A (n=28), followed by -C (n=11), and -B (n=4), including eight HRV-A, one -B and seven -C genotypes. Both RSV-A (n=5) and -B (n=5) were detected. No RSV-A sequences were assigned as ON1, and two samples were assigned BA9 after amino acid alignment indicating characteristic of 20 amino acid duplication, as well as nine substitutions. This study describes the first molecular and phylogenetic characterisation of respiratory viruses in SUDI cases in Africa. Future studies should include identifying circulating HRV and RSV strains associated with clinical disease severity.