Skip to main content

Phylogenetic #discordance cannot identify #genomic #reassortment events: a case study with the avian #influenza virus #H5Nx

Image
By G.M.

Abstract

Recombination plays a central role in the evolution of the RNA virus genome, as it allows the exchange of genetic material between different viral lineages. Reassortment is a form of recombination specific to viruses with segmented genomes that involves the exchange of entire segments between lineages. This process has played a significant role in the adaptation and spread of influenza viruses, where novel combinations of genomic segments are produced from divergent lineages (i.e., antigenic shift). In this study, we investigated reassortment events in a representative sample of n = 11, 765 complete genomes of H5Nx influenza A viruses from avian hosts. Using tanglegrams and subtree-prune-regraft (SPR) methods to quantify discordance between segment trees, we found evidence of widespread reassortment among these genomes that is consistent with previous studies. However, we obtained the comparable numbers of reassortment events when applying the same methods to sequence data simulated in the complete absence of any reassortment. This outcome indicates a high false positive rate in identifying reassortment events due to uncertainty in phylogenetic reconstruction. There was also no significant difference between SPR events inferred from real data versus simulated false positives with respect to subtree size, or the distance between prune and regraft points in the reference tree. Although there is no doubt that reassorment has played a significant role in the origin of new pandemic strains of influenza viruses, these results imply that previous reports of extensive reassortment in the avian influenza virus literature should be interpreted with caution.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.02.24.639875v1

____

Labels:

Comments

Post a Comment

Popular posts from this blog

#Neuroinvasive #Oropouche virus in a patient with #HIV from extra-Amazonian #Brazil

By G.M.
{Excerpt} A novel reassortant Oropouche virus (OROV) lineage (with medium [M], large [L], and small [S] RNA segments : M1L2S2) has driven Brazil's largest and most geographically widespread OROV epidemic , expanding beyond the endemic Amazon basin to establish local transmission across multiple Brazilian states and other previously unaffected Latin American countries . The rapid spread of this lineage underscores its evolutionary potential and reinforces its significance as a public health threat .1 Similar to chikungunya and Zika viruses, expanding arboviruses can exhibit unexpected clinical and epidemiological shifts , including vertical transmissions , neuroinvasive effects, and potentially fatal outcomes.2–4 Although OROV typically causes self-limited febrile illness, accumulating clinical and experimental evidence suggests neurotropic potential .5 This Correspondence describes the first confirmed case of neuroinvasive OROV infection caused by the emergent M1L2S2 lineage in ext...
Post a Comment
Read more »

No evidence of immune #exhaustion after repeated #SARS-CoV-2 #vaccination in vulnerable and healthy populations

By G.M.
Abstract Frequent SARS-CoV-2 vaccination in vulnerable populations has raised concerns that this may contribute to T cell exhaustion , which could negatively affect the quality of immune protection. Herein, we examined the impact of repeated SARS-CoV-2 vaccination on T cell phenotypic and functional exhaustion in frail older adults in long-term care (n = 23), individuals on immunosuppressive drugs (n = 10), and healthy adults (n = 43), in Canada . Spike-specific CD4+ and CD8+ T cell levels did not decline in any cohort following repeated SARS-CoV-2 vaccination, nor did the expression of exhaustion markers on spike-specific or total T cells increase. T cell production of multiple cytokines (i.e. polyfunctionality) in response to the spike protein of SARS-CoV-2 did not decline in any cohort following repeated vaccination. None of the cohorts displayed elevated levels of terminally differentiated T cells following multiple SARS-CoV-2 vaccinations. Thus, repeated SARS-CoV-2 vaccination was...
Post a Comment
Read more »

Chimeric #hemagglutinin and #M2 #mRNA #vaccine for broad #influenza subtype protection

By G.M.
Abstract Since multiple and unpredicted influenza viruses cause seasonal epidemics and even high-risk pandemics , developing a universal influenza vaccine is essential to provide broad protection against various influenza subtypes. Combined with the mRNA lipid nanoparticle-encapsulated (mRNA-LNP) vaccine platform and chimeric immunogen strategy , we developed a novel cocktail mRNA vaccine encoding chimeric HAs (cH5/1-BV, cH7/3) and intact M2 (termed Fluaxe), which confers broad protection against major circulating IAVs and IBVs , as well as highly pathogenic avian influenza . Two-dose intramuscular immunization of Fluaxe in mice elicited cross-reactive neutralizing antibodies , T cell responses, and long-lived immunity, resulting in robust protection against multiple lethal influenza virus infections and severe acute lung injuries . In particular, intramuscular administration stimulated systemic immunity together with a prominent lung tropism of memory cells . Moreover, Fluaxe immuniza...
Post a Comment
Read more »