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. 2024 Oct 21;16(10):1644.
doi: 10.3390/v16101644.

Insights into Genetic and Antigenic Characteristics of Influenza A(H1N1)pdm09 Viruses Circulating in Sicily During the Surveillance Season 2023-2024: The Potential Effect on the Seasonal Vaccine Effectiveness

Fabio Tramuto  1   2 , Carmelo Massimo Maida  1   2 , Giulia Randazzo  2 , Adriana Previti  2 , Giuseppe Sferlazza  2 , Giorgio Graziano  2 , Claudio Costantino  1   2 , Walter Mazzucco  1   2 , Francesco Vitale  1   2
Affiliations

Insights into Genetic and Antigenic Characteristics of Influenza A(H1N1)pdm09 Viruses Circulating in Sicily During the Surveillance Season 2023-2024: The Potential Effect on the Seasonal Vaccine Effectiveness

Fabio Tramuto et al. Viruses. .

Abstract

After disruption in the influenza circulation due to the emergence of SARS-CoV-2, the intensity of seasonal outbreaks has returned to the pre-pandemic levels. This study aimed to evaluate the evolution and variability of whole-genome sequences of A(H1N1)pdm09, the predominant influenza virus in Sicily (Italy) during the season 2023-2024. The potential vaccine efficacy was calculated using the pepitope model based on amino acid changes in the dominant epitope of hemagglutinin. The HA gene sequences showed several amino acid substitutions, some of which were within the major antigenic sites. The phylogenetic analysis showed that Sicilian strains grouped into two main genetic clades (6B.1A.5a.2a.1 and 6B.1A.5a.2a) and several subclades. Notably, about 40% of sequences partially drifted from the WHO-recommended vaccine strain A/Victoria/4897/2022 for the Northern Hemisphere. These sequences mostly belonged to the subclades C.1.8 and C.1.9 and harboured the amino acid mutations responsible for the modest predicted vaccine efficacy (E = 38.12% of 53%, pepitope = 0) against these viruses. Amino acid substitutions in other gene segments were also found. Since influenza viruses are constantly evolving, genomic surveillance is crucial in monitoring their molecular evolution and the occurrence of genetic and antigenic changes, and, thus, their potential impact on vaccine efficacy.

Keywords: Italy; Sicily; antigenic drift; community; influenza virus; molecular surveillance; vaccine efficacy; whole-genome sequencing.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Weekly distribution of influenza A and B laboratory-confirmed cases from October 2023 to June 2024 in Sicily (Italy).
Figure 2
Figure 2
Neighbour-joining phylogenetic tree of HA nucleotide sequences of influenza A(H1N1)pdm09 strains collected in Sicily between October 2023 and April 2024. Solid red circles indicate the study sequences, while A(H1N1)pdm09-like vaccine strains are shown in blue. The strain A/California/7/2009 (GenBank: MN596845) was used as an outgroup. Clades and subclades are defined according to the Nextstrain classification.
Figure 3
Figure 3
Neighbour-joining phylogenetic tree of NA nucleotide sequences of influenza A(H1N1)pdm09 strains collected in Sicily between October 2023 and April 2024. Solid red circles indicate the study sequences, while A(H1N1)pdm09-like vaccine strains are shown in blue. The strain A/California/7/2009 (GenBank: MN596847) was used as an outgroup. Clades and subclades are defined according to the Nextstrain classification.
Figure 4
Figure 4
Lollipop plot of amino acid substitutions in the HA protein of Sicilian A(H1N1)pdm09 circulating during the season 2023/2024, in comparison to the seasonal vaccine strain for the Northern Hemisphere (A/Victoria/4897/2022).
Figure 5
Figure 5
Lollipop plot of amino acid substitutions in the NA protein of Sicilian A(H1N1)pdm09 circulating during the season 2023/2024, in comparison to the seasonal vaccine strain for the Northern Hemisphere (A/Victoria/4897/2022).
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