Jayadas Tibutius Thanesh Pramanayagam, Jeewandara Chandima, Senadheera Bhagya, Kuruppu Heshan, Wickramanayake Rivindu, Bary Farha, Wijewickrama Ananda, Manilgama Suranga, Gamage Manouri, Perera Nilanka, Ogg Graham S, Malavige Gathsaurie Neelika
Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka.
National Institute of Infectious Diseases, Angoda, Sri Lanka.
medRxiv. 2024 Aug 23:2024.08.23.24312476. doi: 10.1101/2024.08.23.24312476.
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.
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.
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.1A.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 3C.2a1b.2a.2a.1b clade and subclade G.1.1.2, while the 2024 sequences were assigned to the 3C.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.
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.
甲型流感因有可能引发大流行而被世界卫生组织列为重点病原体。对流感毒株进行基因组测序，对于了解流感毒株的进化以及选择适用于斯里兰卡不同流感季节的流感疫苗至关重要。因此，我们试图了解斯里兰卡西部省流感病毒的分子流行病学，包括进行突变分析以研究进化动态。
2022年11月至2024年5月，共有349名出现发热和呼吸道症状的个体参与了本研究。采集鼻咽和口咽标本，使用定量PCR检测甲型流感、乙型流感和新冠病毒。使用牛津纳米孔技术对甲型流感毒株进行亚型分型和基因组测序。
49名（14%）患者检测出甲型流感，20名（5.7%）检测出乙型流感，41名（11.7%）检测出新冠病毒。5名参与者出现合并感染。系统发育分析将H1N1 HA基因序列归入6B.1A.5a.2a分支。2023年H1N1序列的HA基因被归入C.1、C.1.2和C.1.8亚分支，而2024年的序列被归入C.1.8和C.1.9亚分支。2023年的H3N2序列被归入3C.2a1b.2a.2a.1b分支和G.1.1.2亚分支，而2024年的序列被归入3C.2a1b.2a.2a.3a.1分支和J.2亚分支。在2023年和2024年的序列中，H1N1出现了K54Q、A186T、Q189E、E224A、R259K、K308R、I418V和X215A氨基酸替换。2024年的H1N1序列还出现了进一步的替换，如V47I、I96T、T120A、A139D、G339X、K156X和T278S。
在这项首次使用基因组测序对斯里兰卡甲型流感毒株进行特征分析的研究中，发现18个月内有不同的甲型流感病毒在传播。由于斯里兰卡的毒株也有一些意义不明的特定突变，继续对斯里兰卡的流感毒株进行详细监测，对于为民众选择最合适的疫苗以及疫苗接种时间至关重要。
