Pakistan has experienced a total of six COVID-19 waves throughout the pandemic, each driven by distinct SARS-CoV-2 lineages. This study explores the introduction of Omicron lineage BA.4 into Pakistan, which contributed to the sixth wave between June and September 2022.
View Article and Find Full Text PDFIn Bayesian phylogenetic and phylodynamic studies it is common to summarise the posterior distribution of trees with a time-calibrated consensus phylogeny. While the maximum clade credibility (MCC) tree is often used for this purpose, we here show that a novel consensus tree method - the highest independent posterior subtree reconstruction, or HIPSTR - contains consistently higher supported clades over MCC. We also provide faster computational routines for estimating both consensus trees in an updated version of TreeAnnotator X, an open-source software program that summarizes the information from a sample of trees and returns many helpful statistics such as individual clade credibilities contained in the consensus tree.
View Article and Find Full Text PDFModern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution. These algorithms require careful evaluation of the quality of the generated samples. Within the field of phylogenetics, one frequently adopted diagnostic approach is to evaluate the and to investigate trace graphs of the sampled parameters.
View Article and Find Full Text PDFInfluenza A viruses have caused more documented global pandemics in human history than any other pathogen. High pathogenicity avian influenza viruses belonging to the H5N1 subtype are a leading pandemic risk. Two decades after H5N1 'bird flu' became established in poultry in Southeast Asia, its descendants have resurged, setting off a H5N1 panzootic in wild birds that is fuelled by: (1) rapid intercontinental spread, reaching South America and Antarctica for the first time; (2) fast evolution via genomic reassortment; and (3) frequent spillover into terrestrial and marine mammals.
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