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Articles by Guy Baele
Spatial patterns of rodent-borne pathogens and ecological suitability of rodent-borne diseases in China
Keywords rodents rodent-borne diseases hyperreservoirs ecological suitability population exposure Introduction Zoonotic diseases originating from wildlife pose a persistent threat to global public health.1–5 Rodents—owing to their widespread distribution, high abundance, and frequent interactions with humans—are key reservoirs and vectors of numerous zoonotic pathogens.6,7 The health risks posed by rodent-borne pathogens are intensifying under global environmental change and expanding human...
Evolutionary history of Jamestown Canyon virus reveals complex multi-vector ecology
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Keywords Jamestown Canyon virus arbovirus phylogenetics sequencing virus evolution disease ecology mosquitoes Introduction Arthropod-borne viruses, or arboviruses, represent a diverse range of pathogens impacting the health of humans and animals.1,2,3 Many arbovirus species remain understudied due to their complex transmission cycles (e.g., a wide range of invertebrate vectors and vertebrate hosts) that present challenges to traditional epidemiological methods.4,5 Among these species, the...
By Ellie Bourgikos, Simon Dellicour, Philippe Lemey, Nicole Feriancek Verified, Angela B. Bransfield, Mallery I. Breban, Michael J. Misencik, Tanya A. Petruff, John Shepard, Theodore G. Andreadis, John Anderson, Kiet A. Ngo, Joseph G. Maffei, Alan P. Dupuis, Stephen M. Rich, Guang Xu, Keith Price, Madeline L. Metzger, Marc A. Suchard, rafael m lopes, Fabiana Gámbaro, Colin J. Carlson, Guy Baele, Alexander T. Ciota, Chantal B.F. Vogels, Philip M. Armstrong, Nathan D. Grubaugh, Gabrielle Sakolsky
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Cell Press
Verified
Circumpolar spread of avian influenza H5N1 to southern Indian Ocean islands - Nature Communications
Abstract Since 2020, the outbreak of high pathogenicity avian influenza (HPAI) H5N1 virus clade 2.3.4.4b has turned into the largest documented panzootic 1,3. Here, we describe its arrival into the Indian Ocean sub-Antarctic archipelagos of Crozet and Kerguelen, where we first detected the virus in October 2024 in dead southern elephant seals. While the panzootic is ongoing, it has already caused unprecedented mortalities of marine mammals and seabirds.
Novel coronaviruses identified in livestock: The urgent need to enhance coronavirus surveillance to mitigate zoonotic risks
Dear Editor, A recent report in this journal on the detection of highly pathogenic avian influenza A (H5N1) virus infection in dairy cattle has renewed concerns regarding livestock farming.1 Livestock farming is shaped by a complex interplay of geographic, economic, cultural, and environmental factors. The global demand for meat, dairy products, and wool has positioned pigs, cattle, and sheep as the dominant species in global farming.
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference - Nature Methods
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Abstract Here we present the open-source and cross-platform BEAST X software that combines molecular phylogenetic reconstruction with complex trait evolution, divergence-time dating and coalescent demographics in an efficient statistical inference engine. BEAST X significantly advances the flexibility and scalability of evolutionary models supported.
By Guy Baele, Xiang Ji, Gabriel W. Hassler, John Mccrone Verified, Zhenyu Zhang, Philippe Lemey, Alexei J Drummond, Andrew Rambaut
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Nature
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International importance and spread of SARS-CoV-2 variants Alpha, Delta, and Omicron BA.1 into Spain - Communications Medicine
Abstract The spread of SARS-CoV-2 has been influenced by multiple factors, from the inherent transmission capabilities of the different variants to the control measurements put in place. Understanding how new variants enter a country is essential for managing future outbreaks. This study investigates how three major variants—Alpha, Delta, and Omicron (BA.1)—entered Spain and how different restrictions potentially affected their introduction.
Navigating sampling bias in discrete phylogeographic analysis: assessing the performance of an adjusted Bayes factor
Abstract Bayesian phylogeographic inference is widely used in molecular epidemiological studies to reconstruct the dispersal history of pathogens. Discrete phylogeographic analysis treats geographic locations as discrete traits and infers lineage transition events among them, and is typically followed by a Bayes factor (BF) test to assess the statistical support.
Prevention and control of avian influenza virus: Recent advances in diagnostic technologies and surveillance strategies - Nature Communications
The natural host for avian influenza virus (AIV) is waterfowl. However, certain subtypes have breached species barriers, causing epizootics in many avian and mammalian species with occasional zoonotic infections in humans. The ongoing spread of highly pathogenic avian influenza (HPAI) A(H5N1) poses a significant and growing public health threat.
HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X
Abstract In 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.
Author Correction: Untangling lineage introductions, persistence and transmission drivers of HP-PRRSV sublineage 8.7 - Nature Communications
Correction to: Nature Communications https://doi.org/10.1038/s41467-024-53076-w, published online 13 October 2024 The original version of this Article contained an error on page 1 in the footnotes for author information in that a statement regarding the joint supervision of the three corresponding authors, Heng Wang, Guy Baele and Guihong Zhang was missing.
Untangling lineage introductions, persistence and transmission drivers of HP-PRRSV sublineage 8.7 - Nature Communications
Abstract Despite a rapid expansion of Porcine reproductive and respiratory syndrome virus (PRRSV) sublineage 8.7 over recent years, very little is known about the patterns of virus evolution, dispersal, and the factors influencing this dispersal. Relying on a national PRRSV surveillance project established over 20 years ago, we expand the available genomic data of sublineage 8.7 from China.
Detecting episodic evolution through Bayesian inference of molecular clock models
Abstract Molecular evolutionary rate variation is a key aspect of the evolution of many organisms that can be modelled using molecular clock models. For example, fixed local clocks revealed the role of episodic evolution in the emergence of SARS-CoV-2 variants of concern. Like all statistical models, however, the reliability of such inferences is contingent on an assessment of statistical evidence. We present a novel Bayesian phylogenetic approach for detecting episodic evolution.
Integrating full and partial genome sequences to decipher the global spread of canine rabies virus - Nature Communications
Abstract Despite the rapid growth in viral genome sequencing, statistical methods face challenges in handling historical viral endemic diseases with large amounts of underutilized partial sequence data. We propose a phylogenetic pipeline that harnesses both full and partial viral genome sequences to investigate historical pathogen spread between countries. Its application to rabies virus (RABV) yields precise dating and confident estimates of its geographic dispersal.
Detecting episodic evolution through Bayesian inference of molecular clock models
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Global disparities in SARS-CoV-2 genomic surveillance - Nature Communications
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Abstract Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries.
By Anderson F. Brito, Elizaveta Semenova, Gytis Dudas, Joses Ho, George Githinji, Charles N. Agoti, Lucy E. Matkin, Charles A. Whittaker, Benjamin P. Howden, Vitali Sintchenko, Tulio de Oliveira, Paola Cristina Resende, Fernando Spilki, Renato Santana Aguiar, Maria Van Kerkhove, Oliver G. Pybus, Seth Flaxman, Marc A. Suchard, Guy Baele
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Nature
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Updated vaccine protects against SARS-CoV-2 variants including Omicron (B.1.1.529) and prevents transmission in hamsters - Nature Communications
Abstract Current COVID-19 vaccines are based on prototypic spike sequences from ancestral 2019 SARS-CoV-2 strains. However, the ongoing pandemic is fueled by variants of concern (VOC) escaping vaccine-mediated protection. Here we demonstrate how immunization in hamsters using prototypic spike expressed from yellow fever 17D (YF17D) as vector blocks ancestral virus (B lineage) and VOC Alpha (B.1.1.7) yet fails to fully protect from Beta (B.1.351).
Multiple-trait subsampling for optimized ancestral trait reconstruction
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Scalable Bayesian phylogenetics
Open AccessReview articles Abstract Recent advances in Bayesian phylogenetics offer substantial computational savings to accommodate increased genomic sampling that challenges traditional inference methods. In this review, we begin with a brief summary of the Bayesian phylogenetic framework, and then conceptualize a variety of methods to improve posterior approximations via Markov chain Monte Carlo (MCMC) sampling.
Context-specific emergence and growth of the SARS-CoV-2 Delta variant - Nature
Genomic data International (non-UK) sequences were downloaded from GISAID on 15 September 2021 and combined with sequences from England taken as part of community surveillance (pillar 2) available from COG-UK as of September 2021. Each week, each of the pillar 2 testing laboratories selected a number of 96-well plates proportional to the fraction of all testing done at the laboratory, for sequencing.
The phylodynamics of SARS-CoV-2 during 2020 in Finland - Communications Medicine
Abstract Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of infections and fatalities globally since its emergence in late 2019. The virus was first detected in Finland in January 2020, after which it rapidly spread among the populace in spring. However, compared to other European nations, Finland has had a low incidence of SARS-CoV-2.
Serum neutralization of SARS-CoV-2 Omicron sublineages BA.1 and BA.2 in patients receiving monoclonal antibodies - Nature Medicine
Abstract The SARS-CoV-2 Omicron BA.1 sublineage has been supplanted in many countries by the BA.2 sublineage. BA.2 differs from BA.1 by about 21 mutations in its spike. Here, we first compared the sensitivity of BA.1 and BA.2 to neutralization by 9 therapeutic monoclonal antibodies (mAbs). In contrast to BA.1, BA.2 was sensitive to Cilgavimab, partly inhibited by Imdevimab and resistant to Adintrevimab and Sotrovimab.
Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak
To understand the implications of EBOV metapopulation dynamics during the 2013–2016 epidemic, we first investigate the impact of hypothetical intervention strategies on epidemic size and duration. To model the effects of reducing long-distance dispersal (e.g. through travel restrictions), we prune the EBOV phylogenetic trees when a long-distance lineage translocation between administrative areas was inferred, by effectively removing transmission following such dispersal events.
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