Genetic diversity and molecular characterization of HRSV-A on the coast of Peru, 2009-2020

The objective of this study was to molecularly characterize human respiratory syncytial virus A (HRSV-A) genotypes that circulated on the coast of Peru between 2009 and 2020.

In total, 1,694 samples were collected from pediatric patients who were hospitalized with acute respiratory infection during the study period. Samples were analyzed by real-time RT-PCR. The second hypervariable region of the G gene was amplified from HRSV-A-positive samples with high viral load and subsequently sequenced for genotyping and molecular characterization. Phylogenetic reconstruction was performed using the maximum likelihood method, and temporal analysis was conducted by Bayesian inference using the Markov chain-based Monte Carlo (MCMC) algorithm.

Of the total samples processed, 341 (20.13%) were positive for HRSV, of which 211 (61.88%) cases were positive for HRSV-A. A total of 53 nucleotide sequences were obtained from the partial G gene, corresponding to the second hypervariable region. Phylogenetic inference together with representative HRSV-A sequences showed the presence of clades assigned to the NA1 (A.3.1 and A.3.1.1) and ON1 (A. D, A. D.1, A. D.1.1, A. D.2.2, and A. D.5) genotypes, with evidence of co-circulation of at least two clades during the same year. A distinct monophyletic subclade within the ON1 clade A. D.1 was also identified in our population and was characterized by three exclusive point mutations (S250F, S267L, and T293I) in the analyzed region of the G protein. In addition, temporal analysis of ON1 sequences estimated an evolutionary rate of approximately 4.59 × 10^-3 substitutions per site per year in the C-terminal third of the G protein and placed the most recent common ancestor of the Peruvian sequences around 2008.39 [95% HPD: 2006.38, 2009.67], approximately 1 year before the earliest ON1-positive samples from our study population.

HRSV-A showed genetic diversity on the coast of Peru, with co-circulation of NA1- and ON1-related clades during the study period. Partial G gene analysis also identified a putative autochthonous variant within ON1 clade A. D.1, characterized by distinctive changes in the amino acid profile, and provided temporal evidence consistent with ON1 diversification. These findings should be interpreted in light of the partial nature of the sequenced region; however, they provide a foundation for molecular surveillance and future genomic studies of RSV in Peru.