#Nomenclature for #tracking of genetic #variation of seasonal #influenza viruses

 

Abstract

Background: 

Genomic surveillance of human seasonal influenza viruses is an essential component of the Global Influenza Surveillance and Response system (GISRS) and informs the recommendations for the seasonal influenza vaccine composition. Phylogenetic analysis of viral genome sequences is used to identify groups of viruses sharing potential antigenic change and computational models are used to predict which viral variants are likely to circulate at high levels in upcoming seasons. To facilitate discussion and reporting of genetic diversity, as well as to communicate antigen recommendations, up-to-date and sufficiently granular definitions of genetic clades are important. 

Methods: 

A nomenclature system for segments 4 (haemagglutinin) and 6 (neuraminidase) of human A(H3N2), A(H1N1)pdm09, and influenza B. 

Results: 

We devised a clade suggestion algorithm that proposes new subclades based on criteria including (i) the number of sequences in the group, (ii) the divergence from the directly ancestral clade, and (iii) the number and quality of amino acid substitutions on the branch leading to the common ancestor of the subclade. Algorithmic clade proposals were reviewed and assigned a systematic hierarchical label consisting of a leading letter, followed by numbers (e.g., G.1.3). Names are kept short by aliasing, that is collapsing prefixes into unique letters. Subclade definitions are shared openly to promote adoption and tool development. Nextclade is supporting this new nomenclature and it is being used routinely by the GISRS network. 

Conclusions: 

With increasing genomic surveillance, the need for up-to-date classification schemes is growing and we hope that the current dynamic proposal will adapt to growing data volumes and aid in simplifying the interpretation of these data.

Competing Interest Statement

RAN has received consulting fees from Moderna TX and BioNTech. DEW is currently employed by GSK.

Funding Statement

This work was supported by core funding from the Francis Crick Institute from Cancer Research UK, the UK Medical Research Council, and the Wellcome Trust.

Source: 

Link: https://www.medrxiv.org/content/10.64898/2025.12.06.25341755v1

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#Nomenclature #updates to the hemagglutinin gene #clade designations resulting from continued #evolution of high pathogenicity avian #influenza #H5 virus clades 2.3.2.1c and 2.3.4.4

 

Abstract

The evolutionary divergence of the A(H5) hemagglutinin (HA) gene of high pathogenicity avian influenza (HPAI) viruses (A/goose/Guangdong/96 lineage) was analyzed by phylogenetic and average pairwise distance methods to identify clades that merit nomenclature updates. Based on this assessment, 12 new clade designations were recommended based on division of clade 2.3.2.1c and 2.3.4.4 viruses, which were reported in Africa, Antarctica, Asia, Europe, the Middle East, the Americas and Oceania since the most recent WHO/WOAH/FAO H5 Evolution Working Group update.

Competing Interest Statement

The authors have declared no competing interest.

Source: 

Link: https://www.biorxiv.org/content/10.1101/2025.11.23.690055v1

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Improving #Influenza #Nomenclature Based on #Transmission Dynamics

Abstract

Influenza A viruses (IAVs) evolve rapidly, exhibit zoonotic potential, and frequently adapt to new hosts, often establishing long-term reservoirs. Despite advancements in genetic sequencing and phylogenetic classification, current influenza nomenclature systems remain static, failing to capture evolving epidemiological patterns. This rigidity has led to delays or misinterpretations in public health responses, economic disruptions, and confusion in scientific communication. The existing nomenclature does not adequately reflect real-time transmission dynamics or host adaptations, limiting its usefulness for public health management. The 2009 H1N1 pandemic exemplified these limitations, as it was mischaracterized as “swine flu” despite sustained human-to-human transmission and no direct pig-to-human transmission reported. This review proposes a real-time, transmission-informed nomenclature system that prioritizes host adaptation and sustained transmissibility (R0 > 1) to align influenza classification with epidemiological realities and risk management. Through case studies of H1N1pdm09, H5N1, and H7N9, alongside a historical overview of influenza naming, we demonstrate the advantages of integrating transmission dynamics into naming conventions. Adopting a real-time, transmission-informed approach will improve pandemic preparedness, strengthen global surveillance, and enhance influenza classification for scientists, policymakers, and public health agencies.

Source: Viruses, https://www.mdpi.com/1999-4915/17/5/633

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