Genomic surveillance and evolutionary dynamics of influenza a virus in Sri Lanka

Abstract

Background: Influenza A has been named as a priority pathogen by the WHO due to the potential to cause pandemics. Genomic sequencing of influenza strains is important to understand the evolution of the influenza strains and also to select the appropriate influenza vaccines to be used in the different influenza seasons in Sri Lanka. Therefore, we sought to understand the molecular epidemiology of the influenza viruses in the Western Province of Sri Lanka, including mutational analysis to investigate the evolutionary dynamics.

Methodology: A total of 349 individuals presenting with fever and respiratory symptoms were enrolled in this study from November 2022 to May 2024. Nasopharyngeal and oropharyngeal specimens were collected and screened using quantitative PCR to detect Influenza A, Influenza B, and SARS-CoV-2. Subtyping and genomic sequencing was carried out on influenza A strains using Oxford Nanopore Technology.

Results: Influenza A was detected in 49 (14%) patients, influenza B in 20 (5.7%) and SARS-CoV-2 in 41 (11.7%). Co-infections were observed in five participants. The phylogenetic analysis assigned the H1N1 HA gene sequences within the 6B.1 A.5a.2a clade. The HA gene of the H1N1 sequences in 2023 were assigned as belonging to the subclades C.1, C.1.2, and C.1.8, while the 2024 sequences were assigned to subclades C.1.8 and C.1.9. The H3N2 sequences from 2023 were assigned to the 3 C.2a1b.2a.2a.1b clade and subclade G.1.1.2, while the 2024 sequences were assigned to the 3 C.2a1b.2a.2a.3a.1 clade and subclade J.2. The K54Q, A186T, Q189E, E224A, R259K, K308R, I418V, and X215A amino acid substitutions were seen in the H1N1 in the 2023 and 2024 sequences. The 2024 H1N1 sequences additionally exhibited further substitutions, such as V47I, I96T, T120A, A139D, G339X, K156X, and T278S.

Conclusion: In this first study using genomic sequencing to characterize the influenza A strains in Sri Lanka, which showed different influenza A viruses circulating in an 18-month period. As the Sri Lankan strains also had certain mutations of unknown significance, it would be important to continue detailed surveillance of the influenza strains in Sri Lanka to choose the most suitable vaccines for the population and the timing of vaccine administration.

Keywords: Clades; Genomic sequencing; Influenza A; Molecular epidemiology; SARS-CoV-2; Severe disease; Subtypes; Vaccines.

Fig. 1

Distribution of influenza A, influenza B, and SARS-CoV-2 infections across different age groups among recruited participants

Fig. 2

Phylogenetic tree of the H1N1 HA gene. The phylogenetic tree was generated with the Sri Lankan H1N1 sequences (n = 14) in comparison to the global H1N1 strains. All the Sri Lankan were assigned to clade 6B.1 A.5a.2a. The H1N1 Sri Lankan sequence clusters are shaded in green, orange and grey shades, while the reference sequences are highlighted in green

Fig. 3

Phylogenetic tree of the H3N2 HA gene. The phylogenetic tree was generated with the Sri Lankan H3N2 sequences (n = 3) in comparison to the global H1N1 strains. The 2023 sequence was assigned to the 3 C.2a1b.2a.2a.1b clade, while the 2024 sequences were assigned to the 3 C.2a1b.2a.2a.3a.1 clade. The H1N1 Sri Lankan sequence clusters are shaded in green, orange and grey shades, while the reference sequences are highlighted in green

Fig. 4

Heatmap of amino acid substitutions in hemagglutinin (HA) and neuraminidase (NA) genes of influenza A H1N1 and H3N2 viruses. (Panels A and B show mutations in the HA and NA genes of H1N1, respectively, while panels C and D display mutations in the HA and NA genes of H3N2. Each row represents an individual virus sequence, identified by its GISAID EPI_ISL accession number, and each column represents a specific amino acid position where mutations have occurred. The presence of a mutation is indicated by a blue square, and the absence by a white square)