Tweet
Proc Biol Sci
. 2024 Aug;291(2028):20240790.
doi: 10.1098/rspb.2024.0790. Epub 2024 Aug 14. Sequence-based detection of emerging antigenically novel influenza A viruses
Alpha Forna 1 2 3 , K Bodie Weedop 1 , Lambodhar Damodaran 3 , Norman Hassell 4 , Rebecca Kondor 4 , Justin Bahl 2 3 , John M Drake # 1 2 5 , Pejman Rohani # 1 2 5 6
Affiliations
The detection of evolutionary transitions in influenza A (H3N2) viruses' antigenicity is a major obstacle to effective vaccine design and development. In this study, we describe Novel Influenza Virus A Detector (NIAViD), an unsupervised machine learning tool, adept at identifying these transitions, using the HA1 sequence and associated physico-chemical properties. NIAViD performed with 88.9% (95% CI, 56.5-98.0%) and 72.7% (95% CI, 43.4-90.3%) sensitivity in training and validation, respectively, outperforming the uncalibrated null model-33.3% (95% CI, 12.1-64.6%) and does not require potentially biased, time-consuming and costly laboratory assays. The pivotal role of the Boman's index, indicative of the virus's cell surface binding potential, is underscored, enhancing the precision of detecting antigenic transitions. NIAViD's efficacy is not only in identifying influenza isolates that belong to novel antigenic clusters, but also in pinpointing potential sites driving significant antigenic changes, without the reliance on explicit modelling of haemagglutinin inhibition titres. We believe this approach holds promise to augment existing surveillance networks, offering timely insights for the development of updated, effective influenza vaccines. Consequently, NIAViD, in conjunction with other resources, could be used to support surveillance efforts and inform the development of updated influenza vaccines.
Keywords: antigenic transition; infectious disease forecasting; influenza virus; unsupervised machine learning; viral evolution.
. 2024 Aug;291(2028):20240790.
doi: 10.1098/rspb.2024.0790. Epub 2024 Aug 14. Sequence-based detection of emerging antigenically novel influenza A viruses
Alpha Forna 1 2 3 , K Bodie Weedop 1 , Lambodhar Damodaran 3 , Norman Hassell 4 , Rebecca Kondor 4 , Justin Bahl 2 3 , John M Drake # 1 2 5 , Pejman Rohani # 1 2 5 6
Affiliations
- PMID: 39140324
- DOI: 10.1098/rspb.2024.0790
The detection of evolutionary transitions in influenza A (H3N2) viruses' antigenicity is a major obstacle to effective vaccine design and development. In this study, we describe Novel Influenza Virus A Detector (NIAViD), an unsupervised machine learning tool, adept at identifying these transitions, using the HA1 sequence and associated physico-chemical properties. NIAViD performed with 88.9% (95% CI, 56.5-98.0%) and 72.7% (95% CI, 43.4-90.3%) sensitivity in training and validation, respectively, outperforming the uncalibrated null model-33.3% (95% CI, 12.1-64.6%) and does not require potentially biased, time-consuming and costly laboratory assays. The pivotal role of the Boman's index, indicative of the virus's cell surface binding potential, is underscored, enhancing the precision of detecting antigenic transitions. NIAViD's efficacy is not only in identifying influenza isolates that belong to novel antigenic clusters, but also in pinpointing potential sites driving significant antigenic changes, without the reliance on explicit modelling of haemagglutinin inhibition titres. We believe this approach holds promise to augment existing surveillance networks, offering timely insights for the development of updated, effective influenza vaccines. Consequently, NIAViD, in conjunction with other resources, could be used to support surveillance efforts and inform the development of updated influenza vaccines.
Keywords: antigenic transition; infectious disease forecasting; influenza virus; unsupervised machine learning; viral evolution.