E. Holmes

Publications882
h-index139
Citations82,735
Highly Influential Citations4,188
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A new coronavirus associated with human respiratory disease in China
TLDR
Phylogenetic and metagenomic analyses of the complete viral genome of a new coronavirus from the family Coronaviridae reveal that the virus is closely related to a group of SARS-like coronaviruses found in bats in China. Expand
Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
TLDR
The phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans. Expand
A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder
TLDR
The observation that irradiated combs from affected colonies can be repopulated with naive bees suggests that infection may contribute to colony collapse disorder (CCD). Expand
The proximal origin of SARS-CoV-2
TLDR
It is shown that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus, and scenarios by which they could have arisen are discussed. Expand
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
TLDR
A rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread and is designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide. Expand
Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins
TLDR
The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of new coronaviruses and should be removed from wet markets to prevent zoonotic transmission. Expand
Rates of evolutionary change in viruses: patterns and determinants
TLDR
It is shown that the high rate of nucleotide substitution in RNA viruses is matched by some DNA viruses, suggesting that evolutionary rates in viruses are explained by diverse aspects of viral biology, such as genomic architecture and replication speed, and not simply by polymerase fidelity. Expand
Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region.
TLDR
A new nomenclature for HCV variants is proposed in this communication that reflects the two-tiered nature of sequence differences between different viral isolates and describes criteria that would enable new variants to be assigned within the classification as they are discovered. Expand
New World Bats Harbor Diverse Influenza A Viruses
TLDR
Using consensus degenerate RT-PCR, a novel influenza A virus is identified in a flat-faced fruit bat from Peru, indicating that bats constitute a potentially important and likely ancient reservoir for a diverse pool of influenza viruses. Expand
HIV evolution: CTL escape mutation and reversion after transmission
TLDR
Data show that the process of accumulation of escape mutations within HIV is not inevitable, and complex epitope- and residue-specific selection forces, including CTL-mediated positive selection pressure and virus-mediated purifying selection, operate in tandem to shape HIV evolution at the population level. Expand
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