Molecular characterization of human Respiratory Syncytial Virus in Mexico (season 2023–2024) through whole-genome sequencing

Background Human respiratory syncytial virus (hRSV) is a one of major cause of severe acute respiratory infection (SARI) mainly in young children and the elderly. Genomic surveillance of hRSV is currently of interest for understanding of viral evolution and the monitoring of genetic variations that may affect transmissibility and pathogenicity. Herein, we sequenced complete genomes of hRSV-A and B from season 2023–2024, isolated from pediatric and adult patients with SARI. Methods One hundred pediatrics and 43 adult hospitalized patients, as well as 14 non-hospitalized adult patients positive to hRSV were enrolled. Libraries of hRSV complete genome were generated and sequenced on a MiSeq platform. Phylogenetic analysis and maximum likelihood trees were constructed with the 81 hRSV A and 29 hRSV B sequences obtained in our study. Additionally, we analyzed the list of non-synonymous substitutions and their frequencies for each of the eleven viral proteins. Results hRSV A was prevalent (68%) and children under five years old was the principal group affected. The hRSV A isolates belonged to the A.D lineage and sub-lineages A.D.1.5, A.D.1.8, A.D.3, and A.D.5.2 were prevalent. The hRSV B subgroup was less diverse since the dominant sub-lineage was B.D.E.1. Amino acid substitutions per viral isolate for each of the eleven viral proteins indicated higher variability in hRSV A compared to hRSV B. As expected, we observed a high diversity of substitutions in proteins G, F and L. Conclusions Several lineages and high rate of mutation mainly in RSV-A were found during winter season 2023–2024 in Mexico. The increasing availability of complete hRSV genome sequences will facilitate the surveillance of specific substitutions, thereby contributing to a better understanding of viral evolution and the effectiveness of prophylactic strategies.