Andrew Rambaut

The paper analyzes the spread of H5N1 B3.13 in U.S. dairy cattle using genomic data and movement networks, finding that cattle movement, not birds, drives the outbreak.

The paper introduces parallel algorithms to improve the computational efficiency of structured coalescent models for phylogeographic analysis, enabling faster and larger-scale studies of pathogen spread.

This study tracks the emergence and molecular evolution of H5N1 influenza viruses in U.S. dairy cattle, identifying increased mutation rates and positive selection after spillover from birds.

This study tracks the spread and evolution of H5N1 in the sub-Antarctic and Antarctica, revealing long-distance dispersal and mammalian-adaptive mutations.

This paper introduces squirrel, a tool for analyzing MPXV genomes to detect outbreaks and classify APOBEC3 mutations, aiding public health responses.

This study models latency in Ebola virus using a novel phylogenetic approach, finding evidence of extended quiescence in the reservoir, which changes understanding of its evolutionary history and geographic spread.

The paper develops ARTIC HELP, an open-source alternative to ARTIC nanopore sequencing protocols using commercial enzymes, achieving comparable genome coverage for SARS-CoV-2 and Norovirus GII with reduced supply chain dependencies.

The paper introduces HIPSTR, a new consensus tree method that outperforms MCC in capturing high-support clades, and presents an updated TreeAnnotator X with faster computational routines.

This study introduces two novel amplicon sequencing schemes for RSV A and B, demonstrating their effectiveness in generating high-quality genomes globally and revealing minimal geographic clustering of RSV sequences.

PrimalScheme provides open-source tools for designing low-cost viral genome sequencing primers, generating over 67,000 schemes and enabling large-scale genomic surveillance.

Reanalysis of public environmental metatranscriptomes from the Huanan market links SARS-CoV-2 positivity to one wildlife stall containing raccoon dog, civet and bamboo rat genetic material.

The paper introduces piranha, a tool for automated detection and classification of polioviruses from nanopore sequencing reads, enabling efficient intratypic differentiation and identification of wild-type and vaccine-derived polioviruses.

This paper introduces a lineage classification system for rabies virus based on SARS-CoV-2 nomenclature, enabling high-resolution tracking of viral spread and improving disease control.

The paper investigates how much Pango lineage information can be inferred from SARS-CoV-2 spike gene sequences and introduces the concept of lineage sets for classification.

This study analyzes SARS-CoV-2 genomic sequences from Rwanda to track variant evolution and regional spread, identifying emerging sub-lineages and VOCs introduced through travel.

MAJORA enables decentralized sequencing and integration of SARS-CoV-2 genomic data and metadata across the COG-UK network, supporting rapid genomic surveillance.

This paper develops an epigenetic clock for wild wood mice using DNA methylation data to estimate age and study ageing rates in the wild.

The paper identifies a deletion mutation in the spike protein of SARS-CoV-2 and examines its presence in clinical and in vitro samples, suggesting potential implications for viral replication and vaccine development.

January 2020 cases in Germany and Washington State were contained, while separate later introductions from China seeded the first sustained SARS-CoV-2 transmission networks in Italy and Washington State.

The paper describes the early response to the SARS-CoV-2 outbreak in the Netherlands, focusing on whole genome sequencing and its role in public health decision making.

SANTA-SIM simulates viral sequence evolution incorporating selection, recombination, and mutation to test inference methods.

This study sequenced 110 Zika virus genomes from 10 countries, revealing rapid expansion in Brazil, multiple introductions into other regions, and undetected circulation before confirmed cases.

The paper uses ZIKV genomes to estimate the origin and spread of Zika virus in Brazil and the Americas, providing a timeframe for baseline microcephaly rates.

This study uses phylogenetic methods and simulations to show that MERS-CoV has undergone recent recombination, suggesting frequent co-infection with distinct lineages, likely in camels.