Phylodynamic and Evolution of the Hemagglutinin (HA) and Neuraminidase (NA) Genes of Influenza A(H1N1) pdm09 Viruses Circulating in the 2009 and 2023 Seasons in Italy
Fabio Scarpa,
Leonardo Sernicola,
Stefania Farcomeni,
Alessandra Ciccozzi,
Daria Sanna,
Marco Casu,
Marco Vitale,
Alessia Cicenia,
Marta Giovanetti,
Chiara Romano,
Francesco Branda,
Massimo Ciccozzi,
Alessandra Borsetti
Affiliations
Fabio Scarpa
Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
Leonardo Sernicola
National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00162 Rome, Italy
Stefania Farcomeni
National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00162 Rome, Italy
Alessandra Ciccozzi
Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
Daria Sanna
Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
Marco Casu
Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
Marco Vitale
Laboratorio di Biologia Molecolare—Fondazione Università Niccolò Cusano, 00166 Rome, Italy
Alessia Cicenia
Laboratorio di Biologia Molecolare—Fondazione Università Niccolò Cusano, 00166 Rome, Italy
Marta Giovanetti
Department of Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, 00128 Rome, Italy
Chiara Romano
Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
Francesco Branda
Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
Massimo Ciccozzi
Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
Alessandra Borsetti
National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00162 Rome, Italy
The influenza A(H1N1) pdm09 virus, which emerged in 2009, has been circulating seasonally since then. In this study, we conducted a comprehensive genome-based investigation to gain a detailed understanding of the genetic and evolutionary characteristics of the hemagglutinin (HA) and neuraminidase (NA) surface proteins of A/H1N1pdm09 strains circulating in Italy over a fourteen-year period from 2009 to 2023 in relation to global strains. Phylogenetic analysis revealed rapid transmission and diversification of viral variants during the early pandemic that clustered in clade 6B.1. In contrast, limited genetic diversity was observed during the 2023 season, probably due to the genetic drift, which provides the virus with a constant adaptability to the host; furthermore, all isolates were split into two main groups representing two clades, i.e., 6B.1A.5a.2a and its descendant 6B.1A.5a.2a.1. The HA gene showed a faster rate of evolution compared to the NA gene. Using FUBAR, we identified positively selected sites 41 and 177 for HA and 248, 286, and 455 for NA in 2009, as well as sites 22, 123, and 513 for HA and 339 for NA in 2023, all of which may be important sites related to the host immune response. Changes in glycosylation acquisition/loss at prominent sites, i.e., 177 in HA and 248 in NA, should be considered as a predictive tool for early warning signs of emerging pandemics, and for vaccine and drug development.
