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

IF 4 3区医学 Q2 VIROLOGY Virology Journal Pub Date : 2024-11-26 DOI:10.1186/s12985-024-02555-z

Tibutius Thanesh Pramanayagam Jayadas, Chandima Jeewandara, Bhagya Senadheera, Heshan Kuruppu, Rivindu Wickramanayake, Padukkage Harshani Chathurangika, Nushara Senatilleke, Navanjana Warnakulasuriya, Farha Bary, Ananda Wijewickrama, Suranga Manilgama, Manouri Gamage, Nilanka Perera, Graham S Ogg, Gathsaurie Neelika Malavige

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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.

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斯里兰卡甲型流感病毒的基因组监测和进化动态。

背景：由于甲型流感有可能导致大流行，因此被世界卫生组织列为优先病原体。流感病毒株的基因组测序对于了解流感病毒株的进化以及在斯里兰卡不同流感季节选择合适的流感疫苗非常重要。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，包括突变分析，以研究进化动态：方法：2022 年 11 月至 2024 年 5 月期间，共有 349 名出现发烧和呼吸道症状的患者参与了这项研究。收集鼻咽和口咽标本，并使用定量 PCR 检测甲型流感、乙型流感和 SARS-CoV-2 。利用牛津纳米孔技术对甲型流感菌株进行了亚型鉴定和基因组测序：结果：49 名患者（14%）检测出甲型流感，20 名患者（5.7%）检测出乙型流感，41 名患者（11.7%）检测出 SARS-CoV-2。有 5 人合并感染。系统发生学分析将 H1N1 HA 基因序列归入 6B.1 A.5a.2a 支系。2023 年的 H1N1 序列的 HA 基因被归入 C.1、C.1.2 和 C.1.8 亚支系，而 2024 年的序列被归入 C.1.8 和 C.1.9 亚支系。2023 年的 H3N2 序列被归入 3 C.2a1b.2a.2a.1b 支系和 G.1.1.2 亚支系，而 2024 年的序列被归入 3 C.2a1b.2a.2a.3a.1 支系和 J.2 亚支系。在 2023 年和 2024 年的序列中，H1N1 出现了 K54Q、A186T、Q189E、E224A、R259K、K308R、I418V 和 X215A 氨基酸置换。2024 年的 H1N1 序列还出现了更多的氨基酸替代，如 V47I、I96T、T120A、A139D、G339X、K156X 和 T278S：本研究首次利用基因组测序技术分析了斯里兰卡甲型流感病毒株的特征，结果显示，在 18 个月的时间里，有不同的甲型流感病毒在斯里兰卡流行。由于斯里兰卡的毒株也存在某些意义不明的变异，因此继续对斯里兰卡的流感毒株进行详细监测，以选择最适合该国人口的疫苗和接种疫苗的时机非常重要。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Virology Journal 医学-病毒学

CiteScore

7.40

自引率

2.10%

发文量

186

审稿时长

1 months

期刊介绍： Virology Journal is an open access, peer reviewed journal that considers articles on all aspects of virology, including research on the viruses of animals, plants and microbes. The journal welcomes basic research as well as pre-clinical and clinical studies of novel diagnostic tools, vaccines and anti-viral therapies. The Editorial policy of Virology Journal is to publish all research which is assessed by peer reviewers to be a coherent and sound addition to the scientific literature, and puts less emphasis on interest levels or perceived impact.