HAN ALVIN

Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)

Published date : 11 Mar 2019

Sub-species nomenclature systems of pathogens are increasingly based on sequence data. The use of phylogenetics to identify and differentiate between clusters of genetically similar pathogens is particularly prevalent in virology from the nomenclature of human papillomaviruses to highly pathogenic avian influenza (HPAI) H5Nx viruses. These nomenclature systems rely on absolute genetic distance thresholds to define the maximum genetic divergence tolerated between viruses designated as closely related.

type
Journal Paper
journal
Molecular Biology and Evolution, 2019 Mar 11. pii: msz053. doi: 10.1093/molbev/msz053
Impact Factor
10.217

Individual immune selection pressure has limited impact on seasonal influenza virus evolution

Published date : 06 Dec 2018

Seasonal influenza viruses are subjected to strong selection as seen by the sequential replacement of existing viral populations on the emergence of new antigenic variants. However, the process of within-host de novo mutant generation and evolutionary selection that underlies these antigenic sweeps is poorly understood. Here, we investigate mutational patterns between evolutionarily closely related human seasonal influenza viruses using host age as a proxy for immune experience.

type
Journal Paper
journal
Nature Ecology & Evolution, 2018, doi: 10.1038/s41559-018-0741-x

The Geographic Variation of Surveillance and Zoonotic Spillover Potential of Influenza Viruses in Domestic Poultry and Swine

Published date : 27 Nov 2018

Background
Avian and swine influenza viruses circulate worldwide and pose threats to both animal and human health. The design of global surveillance strategies is hindered by information gaps on the geospatial variation in virus emergence potential and existing surveillance efforts.

type
Journal Paper
journal
Open Forum Infectious Diseases, Vol. 5, issue 12, 1 Dec 2018, doi: 10.1093/ofid/ofy318
Impact Factor
3.240