Genetic Diversity and Evolutionary Kinetics of Influenza A Virus H3N2 Subtypes Circulating in Riyadh, Saudi Arabia

Presence of a large foreign workforce and the annual gathering of people for pilgrimage
from around the globe have significantly contributed to the emergence and diversity of respiratory
viruses in Saudi Arabia. Here, we report the sequence and phylogenetic analysis of the H3N2 subtype
of influenza A virus (IAV) in clinical samples collected from Riyadh, Saudi Arabia. Based on RT-PCR,
IAV was found in 88 (28.3%) of the 311 samples screened. Of the 88-IAV positive samples, 43 (48.8%)
were H1N1 subtype while the remaining 45 (51.2%) were found to be of the H3N2 subtype. Complete
sequencing of HA and NA genes of H3N2 revealed, twelve and nine amino acid (AA) substitutions
respectively, and importantly, these variations are absent in the current vaccine strains. Based on the
phylogenetic analysis, the majority of H3N2 strains were grouped in the same clades as the vaccine
strains. Importantly, the N-glycosylation sites at AA 135(NSS) were found to be unique to 6 strains
in the investigated HA1 protein and were absent in the current vaccine strains. These data may
have significant clinical implications in designing novel and population-based vaccines for IAV and
underscore the need for regular monitoring of efficacy of vaccines due to emerging variants.